Enopeptins, uses thereof, and methods of snythesis thereof

ABSTRACT

Provided herein are inventive enopeptin compounds of Formula (I): 
     
       
         
         
             
             
         
       
     
     and pharmaceutically acceptable salts thereof, and pharmaceutical compositions thereof. Further provided are methods of preparation, use, and treatment.

RELATED APPLICATIONS

The present application is a continuation of and claims priority under 35 U.S.C. §120 to U.S. Application, U.S. Ser. No. 14/008,062, filed Dec. 9, 2013, which is a national stage filing under 35 U.S.C. §371 of international PCT application, PCT/US2012/031443, filed Mar. 30, 2012, which claims priority under 35 U.S.C. §119(e) to U.S. provisional patent applications, U.S. Ser. No. 61/469,493, filed Mar. 30, 2011, and U.S. Ser. No. 61/477,061, filed Apr. 19, 2011, each of which is incorporated herein by reference.

BACKGROUND OF THE INVENTION

Infectious diseases are the third leading cause of death in developed countries and the second leading cause of death worldwide (see, e.g., World Health Organization (WHO) Geneva, World Health Report (2002); Nathan, Nature (2004) 431:899). The efficacy of many antibacterial drugs has been compromised by the emergence of drug resistant, pathogenic bacteria (see, e.g., National Nosocomial Infections Surveillance (NNIS) System, Am. J. Infect. Control (2004) 32:470). The Infectious Disease Society of America has recently outlined the deadly implications of a growing number of drug-resistant pathogens (see, e.g., Boucher et al., J. Clin. Infect. Dis. (2009) 48:1). Methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE), and penicillin-resistant Streptococcus epidermis are especially worrisome in clinical settings. Unfortunately, the prevalence of multidrug-resistant bacteria has made antibiotics of last resort, like vancomycin, the first-line of therapy. The capacity of bacteria to routinely develop resistance to virtually any antibacterial agent necessitates a continuous search for new drugs. There is much evidence in the literature that natural products derived from microorganisms will continue to be a source of novel antibacterial drugs (see, e.g., Clardy, Nat. Biotechnol. (2006) 24:1541). Although natural products often have chemical properties that are incompatible with chemotherapy, it is possible to use medicinal chemistry as a means to enhance their biological activity and/or pharmacological properties (see, e.g., von Nussbaum et al., Angew. Chem. Int. Ed. (2006) 45:5072).

A recent case where medicinal chemistry was used to improve the activity of a natural product was that of the enopeptins (see, e.g., Hinzen et al., Chem Med Chem (2006) 1:689; U.S. 20050107288). The parent compounds were isolated from the soil-dwelling bacterium Streptomyces sp. RK-1051 and are defined by a 16-membered peptidolactone consisting of five L-amino acids to which a lipophilic polyene side chain is appended (see, e.g., Osada et al., J. Antibiot. (1991) 44:1463). A group of closely related compounds, called A54556 A and B, were isolated from Streptomyces hawaiienesis by a research group at Eli Lilly (U.S. Pat. No. 4,492,650). The enopeptins attracted attention because of their potent activity against drug-resistant bacterial pathogens, including MRSA and VRE (see, e.g., Brötz-Oesterhelt et al., Nat. Med. (2005) 11:1082). The apparent lack of cross-resistance for all antibacterial agents on the market or those in clinical development has been ascribed to a peculiar mechanism of action. The enopeptin antibiotics inhibit cell division and cause cell death by binding and deregulating the activity of the casein lytic protease (ClpP) (see, e.g., Brötz-Oesterhelt, supra). Under normal conditions, this fourteen-subunit protease selectively degrades proteins through a physical and functional association with accessory ATPases that recognize and unfold its substrates (see, e.g., Maurizi et al., Biochemistry (1999) 37:7778; Singh et al., Proc. Natl. Acad. Sci., USA. (2000) 97:8898; Baker et al., Trends Biochem. Sci. (2006) 31:647; Hsiung et al., FEBS Lett. (2007) 581: 3749). In the presence of the enopeptins, ClpP indiscriminately degrades folded cytoplasmic proteins, which ultimately causes cell death (see, e.g., Brötz-Oesterhelt, supra). Recent structural studies indicate that the enopeptins bind the ClpP core structure and cause it to undergo a conformational change that exposes the enzymatic active sites of its subunits (see, e.g., Lee et al., Nature Structural Biology (2010) 17:471-479).

Although the enopeptin natural products have remarkable antibacterial activity in vitro, their chemical lability and poor solubility limit their efficacy in vivo (see, e.g., Hinzen et al., Chem Med Chem (2006) 1:689). Therefore, this continues to be a need for the development and study of new and improved enopeptin compounds.

SUMMARY OF THE INVENTION

The present invention provides novel enopeptin compounds, pharmaceutical compositions thereof, and methods of preparation, use, and treatment using these compounds.

In one aspect, provided is a compound of Formula (I):

or a pharmaceutically acceptable salt thereof; wherein R¹, R², R³, R⁴, R⁵, R⁶, R¹¹, R¹², and m are as defined herein.

In another aspect, provided is a method of preparing a compound of Formula (I), the method comprising providing a compound of Formula (G):

or salt thereof; and coupling the compound of Formula (G), or salt thereof, with a compound of Formula (H)

or salt thereof; to provide a compound of Formula (I), or salt thereof.

In certain embodiments, the compound of Formula (G) is prepared by providing a compound of Formula (E):

or salt thereof, wherein PG⁷ is an amino protecting group; cyclizing the compound of Formula (E), or salt thereof, to provide a compound of Formula (F):

or salt thereof; and deprotecting the compound of Formula (F), or salt thereof, to provide a compound of Formula (G) or salt thereof.

In certain embodiments, the compound of Formula (E) is prepared by providing a compound of Formula (C):

or salt thereof; wherein PG¹ and PG⁷ are amino protecting groups; and PG⁸ is an oxygen protecting group; and deprotecting the compound of Formula (C), or salt thereof, to provide a compound of Formula (E) or salt thereof.

In certain embodiments, the compound of Formula (C) is prepared by providing a compound of Formula (A) and a compound of Formula (B):

or salt thereof; and coupling the compound of Formula (A), or salt thereof, with a compound of Formula (B), or salt thereof, to provide a compound of Formula (C), or salt thereof; wherein PG¹ and PG⁷ are amino protecting groups; and PG⁸ is an oxygen protecting group.

In another aspect, provided is a method of treating a microbial infection in a subject, comprising administering an effective amount of a compound of the present invention, e.g., a compound of Formula (I) or a pharmaceutically acceptable salt thereof, to the subject. In certain embodiments, the microbial infection is a bacterial infection. In certain embodiments, the method further comprises administering the compound in combination with an antibiotic. In certain embodiments, the antibiotic is a ribosome-targeting antibiotic. In certain embodiments, the ribosome-targeting antibiotic is a tetracycline antibiotic.

In another aspect, provided is a method of treating bacterial virulence. Such a method can be conducted in vivo (i.e., by administration to a subject) or in vitro (e.g., upon contact with bacteria in a cell culture). For example, in certain embodiments, provided is a method of treating bacterial virulence comprising administering an effective amount of a compound of the present invention, e.g., a compound of Formula (I) or a pharmaceutically acceptable salt thereof, to a subject with a bacterial infection. In certain embodiments, the compound blocks virulence factor production.

In yet another aspect, provided is a method of treating bacterial infection and/or virulence including the treatment of bacteria or infection caused by bacteria that are resistent to other treatments, are multi-drug tolerant or resistent and/or that neither grow nor die in the presence of or as a result of other treatments. Such a method can be conducted in vivo (i.e., by administration to a subject) or in vitro (e.g., upon contact with bacteria in a cell culture). For example, in certain embodiments, provided is a method of treating bacterial virulence comprising administering an effective amount of a compound of the present invention, e.g., a compound of Formula (I) or a pharmaceutically acceptable salt thereof, to a subject with a bacterial infection. In certain embodiments, the compound blocks virulence factor production.

The details of one or more embodiments of the invention are set forth in the accompanying Figures and the Detailed Description. Other features, objects, and advantages of the invention will be apparent from the description and from the claims.

Definitions Chemical Definitions

Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Organic Chemistry, Thomas Sorrell, University Science Books, Sausalito, 1999; Smith and March March's Advanced Organic Chemistry, 5^(th) Edition, John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive Organic Transformations, VCH Publishers, Inc., New York, 1989; and Carruthers, Some Modern Methods of Organic Synthesis, 3^(rd) Edition, Cambridge University Press, Cambridge, 1987.

Compounds described herein can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., enantiomers and/or diastereomers. For example, the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, E. L. Stereochemistry of Carbon Compounds (McGraw-Hill, NY, 1962); and Wilen, S. H. Tables of Resolving Agents and Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, Ind. 1972). The invention additionally encompasses compounds as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers.

When a range of values is listed, it is intended to encompass each value and sub-range within the range. For example “C₁₋₆ alkyl” is intended to encompass, C₁, C₂, C₃, C₄, C₅, C₆, C₁₋₆, C₁₋₅, C₁₋₄, C₁₋₃, C₁₋₂, C₂₋₆, C₂₋₅, C₂₋₄, C₂₋₃, C₃₋₆, C₃₋₅, C₃₋₄, C₄₋₆, C₄₋₅, and C₅₋₆ alkyl.

As used herein, “alkyl” refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 30 carbon atoms (“C₁₋₃₀ alkyl”). In some embodiments, an alkyl group has 1 to 20 carbon atoms (“C₁₋₂₀ alkyl”). In some embodiments, an alkyl group has 1 to 20 carbon atoms (“C₁₋₁₀ alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“C₁₋₉ alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“C₁₋₈ alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“C₁₋₇ alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“C₁₋₆ alkyl”). In some embodiments, an alkyl group has 1 to 5 carbon atoms (“C₁₋₅ alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms (“C₁₋₄ alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“C₁₋₃ alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“C₁₋₂ alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“C₁ alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C₂₋₆ alkyl”). Examples of C₁₋₆ alkyl groups include methyl (C₁), ethyl (C₂), n-propyl (C₃), isopropyl (C₃), n-butyl (C₄), tert-butyl (C₄), sec-butyl (C₄), iso-butyl (C₄), n-pentyl (C₅), 3-pentanyl (C₅), amyl (C₅), neopentyl (C₅), 3-methyl-2-butanyl (C₅), tertiary amyl (C₅), and n-hexyl (C₆). Additional examples of alkyl groups include n-heptyl (C₇), n-octyl (C₈) and the like. Unless otherwise specified, each instance of an alkyl group is independently unsubstituted (an “unsubstituted alkyl”) or substituted (a “substituted alkyl”) with one or more substituents. In certain embodiments, the alkyl group is an unsubstituted C₁₋₁₀ alkyl (e.g., —CH₃). In certain embodiments, the alkyl group is a substituted C₁₋₁₀ alkyl.

“Perhaloalkyl” is a substituted alkyl group as defined herein wherein all of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. In some embodiments, the alkyl moiety has 1 to 8 carbon atoms (“C₁₋₈ perhaloalkyl”). In some embodiments, the alkyl moiety has 1 to 6 carbon atoms (“C₁₋₈ perhaloalkyl”). In some embodiments, the alkyl moiety has 1 to 4 carbon atoms (“C₁₋₄ perhaloalkyl”). In some embodiments, the alkyl moiety has 1 to 3 carbon atoms (“C₁₋₃ perhaloalkyl”). In some embodiments, the alkyl moiety has 1 to 2 carbon atoms (“C₁₋₂ perhaloalkyl”). In some embodiments, all of the hydrogen atoms are replaced with fluoro. In some embodiments, all of the hydrogen atoms are replaced with chloro. Examples of perhaloalkyl groups include —CF₃, —CF₂CF₃, —CF₂CF₂CF₃, —CCl₃, —CFCl₂, —CF₂Cl, and the like.

As used herein, “alkenyl” refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 30 carbon atoms and one or more carbon-carbon double bonds (“C₂₋₃₀ alkenyl”). In some embodiments, an alkenyl group has 2 to 20 carbon atoms (“C₂₋₂₀ alkenyl”). In some embodiments, an alkenyl group has 2 to 10 carbon atoms (“C₂₋₁₀ alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms (“C₂₋₉ alkenyl”). In some embodiments, an alkenyl group has 2 to 8 carbon atoms (“C₂₋₈ alkenyl”). In some embodiments, an alkenyl group has 2 to 7 carbon atoms (“C₂₋₇ alkenyl”). In some embodiments, an alkenyl group has 2 to 6 carbon atoms (“C₂₋₆ alkenyl”). In some embodiments, an alkenyl group has 2 to 5 carbon atoms (“C₂₋₅ alkenyl”). In some embodiments, an alkenyl group has 2 to 4 carbon atoms (“C₂₋₄ alkenyl”). In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C₂₋₃ alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C₂ alkenyl”). The one or more carbon-carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples of C₂₋₄ alkenyl groups include ethenyl (C₂), 1-propenyl (C₃), 2-propenyl (C₃), 1-butenyl (C₄), 2-butenyl (C₄), butadienyl (C₄), and the like. Examples of C₂₋₆ alkenyl groups include the aforementioned C₂₋₄ alkenyl groups as well as pentenyl (C₅), pentadienyl (C₅), hexenyl (C₆), and the like. Additional examples of alkenyl include heptenyl (C₇), octenyl (C₈), octatrienyl (C₈), and the like. Unless otherwise specified, each instance of an alkenyl group is independently unsubstituted (an “unsubstituted alkenyl”) or substituted (a “substituted alkenyl”) with one or more substituents. In certain embodiments, the alkenyl group is an unsubstituted C₂₋₁₀ alkenyl. In certain embodiments, the alkenyl group is a substituted C₂₋₁₀ alkenyl.

As used herein, “alkynyl” refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 30 carbon atoms and one or more carbon-carbon triple bonds (“C₂₋₃₀ alkynyl”). In some embodiments, an alkynyl group has 2 to 20 carbon atoms (“C₂₋₂₀ alkynyl”). In some embodiments, an alkynyl group has 2 to 10 carbon atoms (“C₂₋₁₀ alkynyl”). In some embodiments, an alkynyl group has 2 to 9 carbon atoms (“C₂₋₉ alkynyl”). In some embodiments, an alkynyl group has 2 to 8 carbon atoms (“C₂₋₈ alkynyl”). In some embodiments, an alkynyl group has 2 to 7 carbon atoms (“C₂₋₇ alkynyl”). In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C₂₋₆ alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms (“C₂₋₅ alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms (“C₂₋₄ alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms (“C₂₋₃ alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms (“C₂ alkynyl”). The one or more carbon-carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl). Examples of C₂₋₄ alkynyl groups include, without limitation, ethynyl (C₂), 1-propynyl (C₃), 2-propynyl (C₃), 1-butynyl (C₄), 2-butynyl (C₄), and the like. Examples of C₂₋₆ alkenyl groups include the aforementioned C₂₋₄ alkynyl groups as well as pentynyl (C₅), hexynyl (C₆), and the like. Additional examples of alkynyl include heptynyl (C₇), octynyl (C₈), and the like. Unless otherwise specified, each instance of an alkynyl group is independently unsubstituted (an “unsubstituted alkynyl”) or substituted (a “substituted alkynyl”) with one or more substituents. In certain embodiments, the alkynyl group is an unsubstituted C₂₋₁₀ alkynyl. In certain embodiments, the alkynyl group is a substituted C₂₋₁₀ alkynyl.

As used herein, “carbocyclyl” refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C₃₋₁₀ carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. In some embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms (“C₃₋₈ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms (“C₅₋₁₀ carbocyclyl”). Exemplary C₃₋₆ carbocyclyl groups include, without limitation, cyclopropyl (C₃), cyclopropenyl (C₃), cyclobutyl (C₄), cyclobutenyl (C₄), cyclopentyl (C₅), cyclopentenyl (C₅), cyclohexyl (C₆), cyclohexenyl (C₆), cyclohexadienyl (C₆), and the like. Exemplary C₃₋₈ carbocyclyl groups include, without limitation, the aforementioned C₃₋₆ carbocyclyl groups as well as cycloheptyl (C₇), cycloheptenyl (C₇), cycloheptadienyl (C₇), cycloheptatrienyl (C₇), cyclooctyl (C₈), cyclooctenyl (C₈), bicyclo[2.2.1]heptanyl (C₇), bicyclo[2.2.2]octanyl (C₈), and the like. Exemplary C₃₋₁₀ carbocyclyl groups include, without limitation, the aforementioned C₃₋₈ carbocyclyl groups as well as cyclononyl (C₉), cyclononenyl (C₉), cyclodecyl (C₁₀), cyclodecenyl (C₁₀), octahydro-1H-indenyl (C₉), decahydronaphthalenyl (C₁₀), spiro[4.5]decanyl (C₁₀), and the like. As the foregoing examples illustrate, in certain embodiments, the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or polycyclic (e.g., containing a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) or tricyclic system (“tricyclic carbocyclyl”)) and can be saturated or can contain one or more carbon-carbon double or triple bonds. “Carbocyclyl” also includes ring systems wherein the carbocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclyl ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system. Unless otherwise specified, each instance of a carbocyclyl group is independently unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a “substituted carbocyclyl”) with one or more substituents. In certain embodiments, the carbocyclyl group is an unsubstituted C₃₋₁₀ carbocyclyl. In certain embodiments, the carbocyclyl group is a substituted C₃₋₁₀ carbocyclyl.

In some embodiments, “carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms (“C₃₋₁₀ cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms (“C₃₋₈ cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms (“C₃₋₆ cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C₅₋₆ cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms (“C₅₋₁₀ cycloalkyl”). Examples of C₅₋₆ cycloalkyl groups include cyclopentyl (C₅) and cyclohexyl (C₅). Examples of C₃₋₆ cycloalkyl groups include the aforementioned C₅₋₆ cycloalkyl groups as well as cyclopropyl (C₃) and cyclobutyl (C₄). Examples of C₃₋₈ cycloalkyl groups include the aforementioned C₃₋₆ cycloalkyl groups as well as cycloheptyl (C₇) and cyclooctyl (C₈). Unless otherwise specified, each instance of a cycloalkyl group is independently unsubstituted (an “unsubstituted cycloalkyl”) or substituted (a “substituted cycloalkyl”) with one or more substituents. In certain embodiments, the cycloalkyl group is an unsubstituted C₃₋₁₀ cycloalkyl. In certain embodiments, the cycloalkyl group is a substituted C₃₋₁₀ cycloalkyl.

As used herein, “heterocyclyl” refers to a radical of a 3- to 14-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“3-14 membered heterocyclyl”). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or polycyclic (e.g., a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”) or tricyclic system (“tricyclic heterocyclyl”)), and can be saturated or can contain one or more carbon-carbon double or triple bonds. Heterocyclyl polycyclic ring systems can include one or more heteroatoms in one or both rings. “Heterocyclyl” also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system. Unless otherwise specified, each instance of heterocyclyl is independently unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a “substituted heterocyclyl”) with one or more substituents. In certain embodiments, the heterocyclyl group is an unsubstituted 3-14 membered heterocyclyl. In certain embodiments, the heterocyclyl group is a substituted 3-14 membered heterocyclyl.

In some embodiments, a heterocyclyl group is a 5-10 membered nonaromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5-8 membered nonaromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heterocyclyl”). In some embodiments, a heterocyclyl group is a 5-6 membered nonaromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heterocyclyl”). In some embodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur.

Exemplary 3-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azirdinyl, oxiranyl, thiorenyl. Exemplary 4-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl. Exemplary 5-membered heterocyclyl groups containing 1 heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl and pyrrolyl-2,5-dione. Exemplary 5-membered heterocyclyl groups containing 2 heteroatoms include, without limitation, dioxolanyl, oxathiolanyl and dithiolanyl. Exemplary 5-membered heterocyclyl groups containing 3 heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary 6-membered heterocyclyl groups containing 1 heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary 6-membered heterocyclyl groups containing 2 heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, dioxanyl. Exemplary 6-membered heterocyclyl groups containing 2 heteroatoms include, without limitation, triazinanyl. Exemplary 7-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl. Exemplary bicyclic heterocyclyl groups include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, tetrahydrobenzothienyl, tetrahydrobenzofuranyl, tetrahydroindolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl, octahydrochromenyl, octahydroisochromenyl, decahydronaphthyridinyl, decahydro-1,8-naphthyridinyl, octahydropyrrolo[3,2-b]pyrrole, indolinyl, phthalimidyl, naphthalimidyl, chromanyl, chromenyl, 1H-benzo[e][1,4]diazepinyl, 1,4,5,7-tetrahydropyrano[3,4-b]pyrrolyl, 5,6-dihydro-4H-furo[3,2-b]pyrrolyl, 6,7-dihydro-5H-furo[3,2-b]pyranyl, 5,7-dihydro-4H-thieno[2,3-c]pyranyl, 2,3-dihydro-1H-pyrrolo[2,3-b]pyridinyl, 2,3-dihydrofuro[2,3-b]pyridinyl, 4,5,6,7-tetrahydro-1H-pyrrolo[2,3-b]pyridinyl, 4,5,6,7-tetrahydrofuro[3,2-c]pyridinyl, 4,5,6,7-tetrahydrothieno[3,2-b]pyridinyl, 1,2,3,4-tetrahydro-1,6-naphthyridinyl, and the like.

As used herein, “aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14π electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“C₆₋₁₄ aryl”). In some embodiments, an aryl group has 6 ring carbon atoms (“C₆ aryl”; e.g., phenyl). In some embodiments, an aryl group has 10 ring carbon atoms (“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). In some embodiments, an aryl group has 14 ring carbon atoms (“C₁₄ aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. Unless otherwise specified, each instance of an aryl group is independently unsubstituted (an “unsubstituted aryl”) or substituted (a “substituted aryl”) with one or more substituents. In certain embodiments, the aryl group is an unsubstituted C₆₋₁₄ aryl. In certain embodiments, the aryl group is a substituted C₆₋₁₄ aryl.

“Aralkyl” is a subset of “alkyl” and refers to an alkyl group, as defined herein, substituted by an aryl group, as defined herein, wherein the point of attachment is on the alkyl moiety.

As used herein, “heteroaryl” refers to a radical of a 5-14 membered monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14π electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur (“5-14 membered heteroaryl”). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryl polycyclic ring systems can include one or more heteroatoms in one or both rings. “Heteroaryl” includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. “Heteroaryl” also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused polycyclic (aryl/heteroaryl) ring system. Polycyclic heteroaryl groups wherein one ring does not contain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and the like) the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indolyl).

In some embodiments, a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In some embodiments, a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In some embodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unless otherwise specified, each instance of a heteroaryl group is independently unsubstituted (an “unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”) with one or more substituents. In certain embodiments, the heteroaryl group is an unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is a substituted 5-14 membered heteroaryl.

Exemplary 5-membered heteroaryl groups containing 1 heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl. Exemplary 5-membered heteroaryl groups containing 2 heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroaryl groups containing 3 heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-membered heteroaryl groups containing 4 heteroatoms include, without limitation, tetrazolyl. Exemplary 6-membered heteroaryl groups containing 1 heteroatom include, without limitation, pyridinyl. Exemplary 6-membered heteroaryl groups containing 2 heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl. Exemplary 6-membered heteroaryl groups containing 3 or 4 heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively. Exemplary 7-membered heteroaryl groups containing 1 heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl. Exemplary 6,6-bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. Exemplary tricyclic heteroaryl groups include, without limitation, phenanthridinyl, dibenzofuranyl, carbazolyl, acridinyl, phenothiazinyl, phenoxazinyl and phenazinyl.

“Heteroaralkyl” is a subset of “alkyl” and refers to an alkyl group, as defined herein, substituted by a heteroaryl group, as defined herein, wherein the point of attachment is on the alkyl moiety.

As used herein, the term “partially unsaturated” refers to a ring moiety that includes at least one double or triple bond. The term “partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl moieties) as herein defined.

As used herein, the term “saturated” refers to a ring moiety that does not contain a double or triple bond, i.e., contains all single bonds.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as defined herein, are optionally substituted (e.g., “substituted” or “unsubstituted” alkyl, “substituted” or “unsubstituted” alkenyl, “substituted” or “unsubstituted” alkynyl, “substituted” or “unsubstituted” carbocyclyl, “substituted” or “unsubstituted” heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or “unsubstituted” heteroaryl group). In general, the term “substituted”, whether preceded by the term “optionally” or not, means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a “substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position. The term “substituted” is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound. The present invention contemplates any and all such combinations in order to arrive at a stable compound. For purposes of this invention, heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.

Exemplary carbon atom substituents include, but are not limited to, halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(aa), —ON(R^(bb))₂, —N(R^(bb))₂, —N(R^(bb))₃ ⁺X, —N(OR^(cc))R^(bb), —SH, —SR^(aa), —SSR^(cc), —C(═O)R^(aa), —CO₂H, —CHO, —C(OR^(cc))₂, —CO₂R^(aa), —OC(═O)R^(aa), —OCO₂R^(aa), —C(═O)N(R^(bb))₂, —OC(═O)N(R^(bb))₂, —NR^(bb)C(═O)R^(aa), —NR^(bb)CO₂R^(aa), —NR^(bb)C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —OC(═NR^(bb))R^(aa), —OC(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —OC(═NR^(bb))N(R^(bb))₂, —NR^(bb)C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa), —NR^(bb)SO₂R^(aa), —SO₂N(R^(bb))₂, —SO₂R^(aa), —SO₂OR^(aa), —OSO₂R^(aa), —S(═O)R^(aa), —OS(═O)R^(aa), —Si(R^(aa))₃, —OSi(Raa)₃—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), —C(═S)SR^(aa), —SC(═S)SR^(aa), —SC(═O)SR^(aa), —OC(═O)SR^(aa), —SC(═O)OR^(aa), —SC(═O)R^(aa), —P(═O)₂R^(aa), —OP(═O)₂R^(aa), —P(═O)(R^(aa))₂, —OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, —OP(═O)₂N(R^(bb))₂, —P(═O)(NR^(bb))₂, —OP(═O)(NR^(bb))₂, —NR^(bb)P(═O)(OR^(cc))₂, —NR^(bb)P(═O)(NR^(bb))₂, —P(R^(cc))₂, —P(R^(cc))₃, —OP(R^(cc))₂, —OP(R^(cc))₃, —B(R^(aa))₂, —B(OR^(cc))₂, —BR^(aa)(OR^(cc)), C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₄ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

or two geminal hydrogens on a carbon atom are replaced with the group ═O, ═S, ═NN(R^(bb))₂, ═NNR^(bb)C(═O)R^(aa), ═NNR^(bb)C(═O)OR^(aa), ═NNR^(bb)S(═O)₂R^(aa), ═NR^(bb), or ═NOR^(cc);

each instance of R^(aa) is, independently, selected from C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, or two R^(aa) groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(bb) is, independently, selected from hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂, —P(═O)(NR^(cc))₂, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, or two R^(bb) groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(cc) is, independently, selected from hydrogen, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, or two R^(cc) groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(dd) is, independently, selected from halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(ee), —ON(R^(ff))₂, —N(R^(ff))₂, —N(R^(ff))₃ ⁺X⁻, —N(OR^(ee))R^(ff), —SH, —SR^(ee), —SSR^(ee), —C(═O)R^(ee), —CO₂H, —CO₂R^(ee), —OC(═O)R^(ee), —OCO₂R^(ee), —C(═O)N(R^(ff))₂, —OC(═O)N(R^(ff))₂, —NR^(ff)C(═O)R^(ee), —NR^(ff)CO₂R^(ee), —NR^(ff)C(═O)N(R^(ff))₂, —C(═NR^(ff))OR^(ee), —OC(═NR^(ff))R^(ee), —OC(═NR^(ff))OR^(ee), —C(═NR^(ff))N(R^(ff))₂, —OC(═NR^(ff))N(R^(ff))₂, —NR^(ff)C(═NR^(ff))N(R^(ff))₂, —NR^(ff)SO₂R^(ee), —SO₂N(R^(ff))₂, —SO₂R^(ee), —SO₂OR^(cc), —OSO₂R^(ee), —S(═O)R^(ee), —Si(R^(ee))₃, —OSi(R^(ee))₃, —C(═S)N(R^(ff))₂, —C(═O)SR^(ee), —C(═S)SR^(ee), —SC(═S)SR^(ee), —P(═O)₂R^(ee), —P(═O)(R^(ee))₂, —OP(═O)(R^(ee))₂, —OP(═O)(OR^(ee))₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, 3-10 membered heterocyclyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups, or two geminal R^(dd) substituents can be joined to form ═O or ═S;

each instance of R^(ee) is, independently, selected from C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀ aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups;

each instance of R^(ff) is, independently, selected from hydrogen, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, 3-10 membered heterocyclyl, C₆₋₁₀ aryl and 5-10 membered heteroaryl, or two R^(ff) groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups; and

each instance of R^(gg) is, independently, halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OC₁₋₆ alkyl, —ON(C₁₋₆ alkyl)₂, —N(C₁₋₆ alkyl)₂, —N(C₁₋₆ alkyl)₃ ⁺X⁻, —NH(C₁₋₆ alkyl)₂ ⁺X⁻, —NH₂(C₁₋₆ alkyl)⁺X⁻, —NH₃ ⁺X⁻, —N(OC₁₋₆ alkyl)(C₁₋₆ alkyl), —N(OH)(C₁₋₆ alkyl), —NH(OH), —SH, —SC₁₋₆ alkyl, —SS(C₁₋₆ alkyl), —C(═O)(C₁₋₆ alkyl), —CO₂H, —CO₂(C₁₋₆ alkyl), —OC(═O)(C₁₋₆ alkyl), —OCO₂(C₁₋₆ alkyl), —C(═O)NH₂, —C(═O)N(C₁₋₆ alkyl)₂, —OC(═O)NH(C₁₋₆ alkyl), —NHC(═O)(C₁₋₆ alkyl), —N(C₁₋₆ alkyl)C(═O)(C₁₋₆ alkyl), —NHCO₂(C₁₋₆ alkyl), —NHC(═O)N(C₁₋₆ alkyl)₂, —NHC(═O)NH(C₁₋₆ alkyl), —NHC(═O)NH₂, —C(═NH)O(C₁₋₆ alkyl), —OC(═NH)(C₁₋₆ alkyl), —OC(═NH)OC₁₋₆ alkyl, —C(═NH)N(C₁₋₆ alkyl)₂, —C(═NH)NH(C₁₋₆ alkyl), —C(═NH)NH₂, —OC(═NH)N(C₁₋₆ alkyl)₂, —OC(NH)NH(C₁₋₆ alkyl), —OC(NH)NH₂, —NHC(NH)N(C₁₋₆ alkyl)₂, —NHC(═NH)NH₂, —NHSO₂(C₁₋₆ alkyl), —SO₂N(C₁₋₆ alkyl)₂, —SO₂NH(C₁₋₆ alkyl), —SO₂NH₂, —SO₂C₁₋₆ alkyl, —SO₂OC₁₋₆ alkyl, —OSO₂C₁₋₆ alkyl, —SOC₁₋₆ alkyl, —Si(C₁₋₆ alkyl)₃, —OSi(C₁₋₆ alkyl)₃-C(═S)N(C₁₋₆ alkyl)₂, C(═S)NH(C₁₋₆ alkyl), C(═S)NH₂, —C(═O)S(C₁₋₆ alkyl), —C(═S)SC₁₋₆ alkyl, —SC(═S)SC₁₋₆ alkyl, —P(═O)₂(C₁₋₆ alkyl), —P(═O)(C₁₋₆ alkyl)₂, —OP(═O)(C₁₋₆ alkyl)₂, —OP(═O)(OC₁₋₆ alkyl)₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀ aryl, 3-10 membered heterocyclyl, 5-10 membered heteroaryl; or two geminal R^(gg) substituents can be joined to form ═O or ═S; wherein X⁻ is a counterion.

As used herein, the term “hydroxyl” or “hydroxy” refers to the group —OH. The term “substituted hydroxyl” or “substituted hydroxyl,” by extension, refers to a hydroxyl group wherein the oxygen atom directly attached to the parent molecule is substituted with a group other than hydrogen, and includes groups selected from —OR^(aa), —ON(R^(bb))₂, —OC(═O)SR^(aa), —OC(═O)R^(aa), —OCO₂R^(aa), —OC(═O)N(R^(bb))₂, —OC(═NR^(bb))R^(aa), —OC(═NR^(bb))OR^(aa), —OC(═NR^(bb))N(R^(bb))₂, —OS(═O)R^(aa), —OSO₂R^(aa), —OSi(R^(aa))₃, —OP(R^(cc))₂, —OP(R^(cc))₃, —OP(═O)₂R^(aa), —OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂, —OP(═O)₂N(R^(bb))₂, and —OP(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as defined herein.

As used herein, the term “thiol” or “thio” refers to the group —SH. The term “substituted thiol” or “substituted thio,” by extension, refers to a thiol group wherein the sulfur atom directly attached to the parent molecule is substituted with a group other than hydrogen, and includes groups selected from —SR^(aa), —S═SR^(cc), —SC(═S)SR^(aa), —SC(═O)SR^(aa), —SC(═O)OR^(aa), and —SC(═O)R^(aa), wherein R^(aa) and R^(cc) are as defined herein.

As used herein, the term, “amino” refers to the group —NH₂. The term “substituted amino,” by extension, refers to a monosubstituted amino, a disubstituted amino, or a trisubstituted amino, as defined herein.

As used herein, the term “monosubstituted amino” refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with one hydrogen and one group other than hydrogen, and includes groups selected from —NH(R^(bb)), —NHC(═O)R^(aa), —NHCO₂R^(aa), —NHC(═O)N(R^(bb))₂, —NHC(═NR^(bb))N(R^(bb))₂, —NHSO₂R^(aa), —NHP(═O)(OR^(cc))₂, and —NHP(═O)(NR^(bb))₂, wherein R^(aa), R^(bb) and R^(cc) are as defined herein, and wherein R^(bb) of the group —NH(R^(bb)) is not hydrogen.

As used herein, the term “disubstituted amino” refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with two groups other than hydrogen, and includes groups selected from —N(R^(bb))₂, —NR^(bb)C(═O)R^(aa), —NR^(bb)CO₂R^(aa), —NR^(bb)C(═O)N(R^(bb))₂, —NR^(bb)C(═NR^(bb))N(R^(bb))₂, —NR^(bb)SO₂R^(aa), —NR^(bb)P(═O)(OR^(cc))₂, and —NR^(bb)P(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as defined herein, with the proviso that the nitrogen atom directly attached to the parent molecule is not substituted with hydrogen.

As used herein, the term “trisubstituted amino” refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with three groups, and includes groups selected from —N(R^(bb))₃ and —N(R^(bb))₃ ⁺X⁻, wherein R^(bb) and X⁻ are as defined herein.

As used herein, the term “sulfonyl” refers to a group selected from —SO₂N(R^(bb))₂, —SO₂R^(aa), and —SO₂OR^(aa), wherein R^(aa) and R^(bb) are as defined herein.

As used herein, the term “sulfinyl” refers to the group —S(═O)R^(aa), wherein R^(aa) is as defined herein.

As used herein, the term “acyl” refers a group wherein the carbon directly attached to the parent molecule is sp² hybridized, and is substituted with an oxygen, nitrogen or sulfur atom, e.g., a group selected from ketones (—C(═O)R^(aa)), carboxylic acids (—CO₂H), aldehydes (—CHO), esters (—CO₂R^(aa), —C(═O)SR^(aa), —C(═S)SR^(aa)), amides (—C(═O)N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa), —C(═S)N(R^(bb))₂), and imines (—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa)), —C(═NR^(bb))N(R^(bb))₂), wherein R^(aa) and R^(bb) are as defined herein.

As used herein, the term “silyl” refers to the group —Si(R^(aa))₃, wherein R^(aa) is as defined herein.

As used herein, the term “boronyl” refers to boranes, boronic acids, boronic esters, borinic acids, and borinic esters, e.g., boronyl groups of Formula —B(R^(aa))₂, —B(OR^(cc))₂, and —BR^(aa)(OR^(cc)), wherein R^(aa) and R^(cc) are as defined herein.

As used herein, the term “halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro, —Cl), bromine (bromo, —Br), or iodine (iodo, —I).

As used herein, a “counterion” is a negatively charged group associated with a positively charged quarternary amine in order to maintain electronic neutrality. Exemplary counterions include halide ions (e.g., F, Cl, Br, I), NO₃, ClO₄, OH, H₂PO₄, HSO₄, sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonic acid-2-sulfonate, and the like), and carboxylate ions (e.g., acetate, ethanoate, propanoate, benzoate, glycerate, lactate, tartrate, glycolate, and the like).

Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quarternary nitrogen atoms. Exemplary nitrogen atom substitutents include, but are not limited to, hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(bb))R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂, —P(═O)(NR^(cc))₂, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, or two R^(cc) groups attached to an N atom are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb), R^(cc) and R^(dd) are as defined above.

In certain embodiments, the substituent present on the nitrogen atom is an amino protecting group (also referred to herein as a “nitrogen protecting group”). Amino protecting groups include, but are not limited to, —OH, —OR^(aa), —N(R^(cc))₂, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(cc))R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), C₁₋₁₀ alkyl (e.g., aralkyl, heteroaralkyl), C₂ ₁₀ alkenyl, C₂ ₁₀ alkynyl, C₃ ₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aralkyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb), R^(cc) and R^(dd) are as defined herein. Amino protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley & Sons, 1999, incorporated herein by reference.

For example, amino protecting groups such as amide groups (e.g., —C(═O)R^(aa)) include, but are not limited to, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, p-phenylbenzamide, o-nitophenylacetamide, o-nitrophenoxyacetamide, acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide, 3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide, 2-methyl-2-(o-nitrophenoxy)propanamide, 2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide, 3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethionine derivative, o-nitrobenzamide and o-(benzoyloxymethyl)benzamide.

Amino protecting groups such as carbamate groups (e.g., —C(═O)OR^(aa)) include, but are not limited to, methyl carbamate, ethyl carbamante, 9-fluorenylmethyl carbamate (Fmoc), 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethyl carbamate, 2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethyl carbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate, 1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC), 1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC), 1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc), 1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and 4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethyl carbamate, t-butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz), p-nitobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzyl carbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzyl carbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate, 2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methyl carbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc), 2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate (Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc), 1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate, p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate, 2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate, 3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methyl carbamate, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate, 2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzyl carbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate, 1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate, 2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate, 1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate, 1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate, 1-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethyl carbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate, p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate, 4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzyl carbamate.

Amino protecting groups such as sulfonamide groups (e.g., —S(═O)₂R^(aa)) include, but are not limited to, p-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide (Ms), β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide, 4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.

Other amino protecting groups include, but are not limited to, phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacyl derivative, N′-phenylaminothioacyl derivative, N-benzoylphenylalanyl derivative, N-acetylmethionine derivative, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted 3,5-dinitro-4-pyridone, N-methylamine, N-allylamine, N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine, N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammonium salts, N-benzylamine, N-di(4-methoxyphenyl)methylamine, N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr), N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr), N-9-phenylfluorenylamine (PhF), N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm), N-2-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine, N-benzylideneamine, N-p-methoxybenzylideneamine, N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine, N-(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine, N-p-nitrobenzylideneamine, N-salicylideneamine, N-5-chlorosalicylideneamine, N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine, N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine, N-borane derivative, N-diphenylborinic acid derivative, N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper chelate, N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate, benzenesulfenamide, o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide, triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys).

In certain embodiments, the substituent present on an oxygen atom is a hydroxyl or thiol protecting group (also respectively referred to herein as an “oxygen protecting group” or “sulfur protecting group”). Hydroxyl and thiol protecting groups include, but are not limited to, —R^(aa), —N(R^(bb))₂, —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂, —C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃, —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and —P(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as defined herein. Hydroxyl and thiol protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley & Sons, 1999, incorporated herein by reference.

Exemplary hydroxyl and thiol protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl (MTHP), 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranyl S,S-dioxide, 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (CTMP), 1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl, 1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl, 2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl, t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl, benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl, p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl, p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido, diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl, triphenylmethyl, α-naphthyldiphenylmethyl, p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl, tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl, 4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl, 4,4′,4″-tris(levulinoyloxyphenyl)methyl, 4,4′,4″-tris(benzoyloxyphenyl)methyl, 3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl, 1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl, 9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl, 1,3-benzodithiolan-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, t-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl, diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 3-phenylpropionate, 4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate (TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec), 2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkyl p-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o-nitrobenzyl carbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate, 4-ethoxy-1-napththyl carbonate, methyl dithiocarbonate, 2-iodobenzoate, 4-azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate, 2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl, 4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate, 2,6-dichloro-4-methylphenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate, o-(methoxyacyl)benzoate, α-naphthoate, nitrate, alkyl N,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts).

These and other exemplary substituents are described in more detail in the Detailed Description, Examples, and claims. The invention is not intended to be limited in any manner by the above exemplary listing of substituents.

Other Definitions

As used herein, the term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al., describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences (1977) 66:1-19. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N⁺(C₁₋₄alkyl)₄ salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.

The term “salt” refers to any and all salts, including pharmaceutically acceptable salts.

A “subject” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g, infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult)) and/or other non-human animals, for example mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs), birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys), reptiles, amphibians, and fish. In certain embodiments, the non-human animal is a mammal. The non-human animal may be a male or female and at any stage of development. A non-human animal may be a transgenic animal.

As used herein, and unless otherwise specified, the terms “treat,” “treating” and “treatment” contemplate an action that occurs while a subject is suffering from the specified infection which reduces the severity of the infection or retards or slows the progression of the infection (“therapeutic treatment”), and also contemplates an action that occurs before a subject begins to suffer from the specified infection and which inhibits or reduces the severity of the infection (“prophylactic treatment”).

In general, the “effective amount” of a compound refers to an amount sufficient to elicit the desired biological response, i.e., treating an infection. As will be appreciated by those of ordinary skill in this art, the effective amount of a compound of the invention may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age, health, and condition of the subject. For example, the effective amount of a compound with anti-bacterial activity is the amount that results in a sufficient concentration to inhibit the growth, reduce, or kill bacteria, or make bacteria less virulent. An effective amount encompasses therapeutic and prophylactic treatment.

As used herein, and unless otherwise specified, a “therapeutically effective amount” of a compound is an amount sufficient to provide a therapeutic benefit in the treatment of a infection or to delay or minimize one or more symptoms associated with the infection. A therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the infection. The term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of infection, or enhances the therapeutic efficacy of another therapeutic agent.

As used herein, and unless otherwise specified, a “prophylactically effective amount” of a compound is an amount sufficient to prevent an infection, or one or more symptoms associated with the infection or prevent its recurrence. A prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the infection. The term “prophylactically effective amount” can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.

As used herein “virulence” refers to the degree of pathogenicity within of a microorganism as indicated by case fatality rates and/or the ability of the organism to invade the issues of the subject; e.g., the ability of the organism to cause an infection. A “reduction of virulence” refers to a reduction of this pathogenic capacity of the organism.

As used herein, use of the phrase “at least one instance” refers to one instance, but also encompasses a range, e.g., for example, from one instance to four instances.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts natural products Enopeptin A and B (Strepomyces sp RK-1051), A54556A and B (Streptomyces hawaiiensis), and synthetic analog ADEP4.

FIG. 2 depicts the retrosynthetic approach to obtain the inventive enopeptin compounds described herein.

FIG. 3 depicts the two approaches used to obtain tripeptide fragments, i.e., using the Ugi four-component reaction (4CR) or the Joullié-Ugi three-component reaction (3CR).

FIGS. 4A-4C depict the synthetic approach to provide pipecolate-derived enopeptin compounds. FIG. 4A: Synthesis of tripeptide fragment using Joullié-Ugi 3CR; FIG. 4B: Coupling of the tripeptide fragment with the ester fragment and ring cyclization; FIG. 4C: Exemplary picolate-derived enopeptin compounds 10a-10d.

FIGS. 5A-5C depict the synthetic approach to provide α,α-disubstituted amino acid-derived enopeptin compounds. FIG. 5A: Synthesis of tripeptide fragment using Ugi 4CR; FIG. 5B: Coupling of the tripeptide fragment with the ester fragment and ring cyclization; FIG. 5C: Exemplary α,α-disubstituted amino acid-derived enopeptin compounds 10e-10h.

FIG. 6 depicts an illustration of the mechanism of action of ClpP (peptidase). ClpP is a multi-subunit protease with internally oriented active sites. ATP-dependent unfoldases unfold proteins (substrates) that are targeted for proteolysis and translocate them into the proteolytic chamber of ClpP (see Baker et al., Trends Biochemical Sciences (2006) 31:647-653).

FIGS. 7A-7B illustrate the crystal structure of enopeptin derivatives in complex with B. subtilis ClP. These molecules make extensive hydrophobic contacts with ClpP. FIG. 7A illustrates ADEP1 bound to ClpP; FIG. 7B illustrates ADEP2 bound to ClpP (see Lee et al., Nature Structural Biology (2010) 17:471-479).

FIG. 8 depicts synthetic enopeptin analogs of interest. Targeted changes to the N-acyl phenylalanine side chain that are expected to affect ClpP binding and thus the biological mechanism.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

The present invention provides inventive enopeptin compounds, e.g. a compound of Formula (I):

or a pharmaceutically acceptable salt thereof; wherein:

R¹ is selected from hydrogen optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl;

R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted heterocyclyl; or

R² and R³ are joined to form a spiro-fused optionally substituted carbocyclyl or spiro-fused optionally substituted heterocyclyl, and R⁴ is hydrogen, optionally substituted alkyl, or an amino protecting group; or

R² and R³ are independently hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl, provided that R² and R³ are not both hydrogen; and R⁴ is hydrogen, optionally substituted alkyl, or an amino protecting group;

R⁵ is —OH, —SH, —NH₂, substituted hydroxyl, substituted thiol, substituted amino, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl;

each instance of R⁶ is independently halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl;

m is 0 or an integer of between 1 and 5, inclusive;

R¹¹ is hydrogen, —OH, —SH, —NH₂, substituted hydroxyl, substituted thiol, substituted amino, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; and

R¹² is hydrogen, —OH, —SH, —NH₂, substituted hydroxyl, substituted thiol, substituted amino, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.

In certain embodiments, the stereochemistry of the carbon attached to R² and R³ may be (R) or (S). In certain embodiments, the stereochemistry of the carbon attached to R² and R³ is (R). In certain embodiments, the stereochemistry of the carbon attached to R² and R³ is (S).

In certain embodiments, R¹ is hydrogen or optionally substituted alkyl. In certain embodiments, R¹ is hydrogen. In certain embodiments, R¹ is optionally substituted alkyl (e.g., —CH₃, —CH₂CH₃).

In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted 5- to 6-membered heterocyclyl.

In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted 5- to 6-membered heterocyclyl, wherein the optionally substituted 5- to 6-membered heterocyclyl contains one or more additional heteroatoms selected from oxygen, nitrogen and sulfur. In certain embodiments, the optionally substituted 5- to 6-membered heterocyclyl contains one additional heteroatom selected from oxygen. In certain embodiments, the optionally substituted 5- to 6-membered heterocyclyl contains one additional heteroatom selected from nitrogen. In certain embodiments, the optionally substituted 5- to 6-membered heterocyclyl contains one additional heteroatom selected from sulfur.

In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted 5- to 6-membered heterocyclyl, wherein the optionally substituted 5- to 6-membered heterocyclyl is partially unsaturated. Alternatively, in certain embodiments, the optionally substituted 5- to 6-membered heterocyclyl is saturated.

In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted 6-membered heterocycyl. In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted piperidinyl. In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form a substituted piperidinyl.

In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted 5-membered heterocycyl. In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted pyrrolidinyl. In certain embodiments, R² is hydrogen, and R³ and R⁴ are joined to form a substituted pyrrolidinyl.

For example, in certain embodiments, wherein R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted heterocyclyl, the compound of Formula (I) is of Formula (II):

or a pharmaceutically acceptable salt thereof; wherein:

each instance of R⁷ is independently selected from the group consisting of halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl;

n is 0 or an integer of between 1 and 8, inclusive; and s is 0 or 1.

For example, in certain embodiments, wherein n is 1, the compound of Formula (II) is a compound of Formula (II-a):

or a pharmaceutically acceptable salt thereof.

In certain embodiments of Formula (I) and (II), the carbon attached to R² and R³ has (S) stereochemistry, e.g., to provide a compound of Formula (II-b):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, s is 0, i.e., to provide an optionally substituted pyrrolidinyl. In this instance, in certain embodiments, n is 0, i.e., to provide an unsubstituted pyrrolidinyl. In certain embodiments, n is an integer of between 1 and 8, inclusive, i.e., to provide a substituted pyrrolidinyl. In certain embodiments, n is an integer of between 1 and 7, inclusive. In certain embodiments, n is an integer of between 1 and 6, inclusive. In certain embodiments, n is an integer of between 1 and 5, inclusive. In certain embodiments, n is an integer of between 1 and 4, inclusive. In certain embodiments, n is an integer of between 1 and 3, inclusive. In certain embodiments, n is an integer of between 1 and 2, inclusive. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4.

In certain embodiments, s is 1, i.e., to provide an optionally substituted piperidinyl. In this instance, in certain embodiments, n is 0, i.e., to provide an unsubstituted piperidinyl. In certain embodiments, n is an integer of between 1 and 8, inclusive, i.e., to provide a substituted piperidinyl. In certain embodiments, n is an integer of between 1 and 7, inclusive. In certain embodiments, n is an integer of between 1 and 6, inclusive. In certain embodiments, n is an integer of between 1 and 5, inclusive. In certain embodiments, n is an integer of between 1 and 4, inclusive. In certain embodiments, n is an integer of between 1 and 3, inclusive. In certain embodiments, n is an integer of between 1 and 2, inclusive. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4.

As generally defined above, each instance of R⁷ is independently selected from the group consisting of halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl.

In certain embodiments, each instance of R⁷ is independently selected from the group consisting of halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, or boronyl. In certain embodiments, at least one instance of R⁷ is halogen. In certain embodiments, at least one instance of R⁷ is —OH. In certain embodiments, at least one instance of R⁷ is —SH. In certain embodiments, at least one instance of R⁷ is —NH₂. In certain embodiments, at least one instance of R⁷ is —CN. In certain embodiments, at least one instance of R⁷ is —NO₂. In certain embodiments, at least one instance of R⁷ is —N₃. In certain embodiments, at least one instance of R⁷ is —SO₂H. In certain embodiments, at least one instance of R⁷ is —SO₃H. In certain embodiments, at least one instance of R⁷ is independently substituted hydroxyl. In certain embodiments, at least one instance of R⁷ is substituted thiol. In certain embodiments, at least one instance of R⁷ is substituted amino. In certain embodiments, at least one instance of R⁷ is sulfonyl. In certain embodiments, at least one instance of R⁷ is sulfinyl. In certain embodiments, at least one instance of R⁷ is acyl. In certain embodiments, at least one instance of R⁷ is silyl. In certain embodiments, at least one instance of R⁷ is boronyl.

In certain embodiments, each instance of R⁷ is independently selected from the group consisting of optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl. In certain embodiments, each instance of R⁷ is independently selected from the group consisting of optionally substituted alkyl, optionally substituted alkenyl, and optionally substituted alkynyl.

In certain embodiments, at least one instance of R⁷ is optionally substituted alkyl. In certain embodiments, at least one instance of R⁷ is unsubstituted alkyl. In certain embodiments, at least one instance of R⁷ is substituted alkyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₁₋₁₀alkyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₁₋₈alkyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₁₋₆alkyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₁₋₄alkyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₁₋₃alkyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₁₋₂alkyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₁alkyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂alkyl. In certain embodiments, at least one instance of R⁷ is —CH₃, —CH₂CH₃, —CH(CH₃)₂, —CH₂CH₂CH₃, or —C(CH₃)₃, —CH₂CH(CH₃)₂, or —CH₂CH₂CH(CH₃)₂.

In certain embodiments, at least one instance of R⁷ is optionally substituted alkenyl. In certain embodiments, at least one instance of R⁷ is unsubstituted alkenyl. In certain embodiments, at least one instance of R⁷ is substituted alkenyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₁₀alkenyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₈alkenyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₆alkenyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₄alkenyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₃alkenyl.

In certain embodiments, at least one instance of R⁷ is optionally substituted alkynyl. In certain embodiments, at least one instance of R⁷ is unsubstituted alkynyl. In certain embodiments, at least one instance of R⁷ is substituted alkynyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₁₀alkynyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₈alkynyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₆alkynyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₄alkynyl. In certain embodiments, at least one instance of R⁷ is optionally substituted C₂₋₃alkynyl.

In certain embodiments, at least one instance of R⁷ is optionally substituted carbocyclyl.

In certain embodiments, at least one instance of R⁷ is optionally substituted heterocyclyl.

In certain embodiments, at least one instance of R⁷ is optionally substituted aryl.

In certain embodiments, at least one instance of R⁷ is optionally substituted heteroaryl.

In certain embodiments of Formula (II), R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted piperidinyl, i.e., to provide a compound of Formula (III):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, wherein n is 1, the compound of Formula (III) is a compound of Formula (III-a):

or a pharmaceutically acceptable salt thereof.

In certain embodiments of Formula (I) and (III), the carbon attached to R² and R³ has (S) stereochemistry, e.g., to provide a compound of Formula (III-b):

or a pharmaceutically acceptable salt thereof.

In certain embodiments of Formula (II), R² is hydrogen, and R³ and R⁴ are joined to form an optionally substituted pyrrolidinyl, i.e., to provide a compound of Formula (IV):

or a pharmaceutically acceptable salt thereof.

For example, in certain embodiments, wherein n is 0, the compound of Formula (IV) is a compound of Formula (IV-a):

or a pharmaceutically acceptable salt thereof.

In certain embodiments of Formula (I) and (IV), the carbon attached to R² and R³ has (S) stereochemistry, e.g., to provide a compound of Formula (IV-b):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted carbocyclyl or spiro-fused optionally substituted heterocyclyl, and R⁴ is hydrogen, optionally substituted alkyl, or an amino protecting group.

In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted heterocyclyl, and R⁴ is hydrogen, optionally substituted alkyl, or an amino protecting group. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 3-7 membered heterocyclyl. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 4-6 membered heterocyclyl. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 5-membered heterocyclyl. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 6-membered heterocyclyl. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 7-membered heterocyclyl. In certain embodiments, the spiro-fused substituted heterocyclyl is substituted.

In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted carbocyclyl and R⁴ is hydrogen, optionally substituted alkyl, or an amino protecting group. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 3-7 membered carbocyclyl. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 4-6 membered carbocyclyl. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 5-membered carbocyclyl. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 6-membered carbocyclyl. In certain embodiments, R² and R³ are joined to form a spiro-fused optionally substituted 7-membered carbocyclyl. In certain embodiments, the spiro-fused substituted carbocyclyl is substituted.

In certain embodiments, R⁴ is hydrogen. In certain embodiments, R⁴ is optionally substituted alkyl (e.g., —CH₃, —CH₂CH₃). In certain embodiments, R⁴ is an amino protecting group as defined herein.

In certain embodiments, wherein R² and R³ are joined to form a spiro-fused optionally substituted carbocyclyl, the compound of Formula (I) is a compound of Formula (V):

or a pharmaceutically acceptable salt thereof,

wherein each instance of R⁸ is independently halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, ═O, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl;

q is 0 or an integer of between 1 and 4, inclusive; and

t is 0 or an integer of between 1 and 4, inclusive.

In certain embodiments, each instance of R⁸ is independently selected from halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, ═O, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl or boronyl. In certain embodiments, at least one instance of R⁸ is halogen. In certain embodiments, at least one instance of R⁸ is —OH. In certain embodiments, at least one instance of R⁸ is —SH. In certain embodiments, at least one instance of R⁸ is —NH₂. In certain embodiments, at least one instance of R⁸ is —CN. In certain embodiments, at least one instance of R⁸ is —NO₂. In certain embodiments, at least one instance of R⁸ is —N₃. In certain embodiments, at least one instance of R⁸ is —SO₂H. In certain embodiments, at least one instance of R⁸ is —SO₃H. In certain embodiments, at least one instance of R⁸ is substituted hydroxyl. In certain embodiments, at least one instance of R⁸ is substituted thiol. In certain embodiments, at least one instance of R⁸ is substituted amino. In certain embodiments, at least one instance of R⁸ is sulfonyl. In certain embodiments, at least one instance of R⁸ is sulfinyl. In certain embodiments, at least one instance of R⁸ is acyl. In certain embodiments, at least one instance of R⁸ is silyl. In certain embodiments, at least one instance of R⁸ is boronyl. In certain embodiments, at least one instance of R⁸ is ═O.

In certain embodiments, each instance of R⁸ is independently optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl. In certain embodiments, each instance of R⁸ is independently optionally substituted alkyl, optionally substituted alkenyl, or optionally substituted alkynyl.

In certain embodiments, at least one instance of R⁸ is optionally substituted alkyl. In certain embodiments, at least one instance of R⁸ is unsubstituted alkyl. In certain embodiments, at least one instance of R⁸ is substituted alkyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₁₋₁₀alkyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₁₋₈alkyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₁₋₆alkyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₁₋₄alkyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₁₋₃alkyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₁₋₂alkyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₁alkyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂alkyl. In certain embodiments, at least one instance of R⁸ is —CH₃, —CH₂CH₃, —CH(CH₃)₂, —CH₂CH₂CH₃, or —C(CH₃)₃, —CH₂CH(CH₃)₂, or —CH₂CH₂CH(CH₃)₂.

In certain embodiments, at least one instance of R⁸ is optionally substituted alkenyl. In certain embodiments, at least one instance of R⁸ is unsubstituted alkenyl. In certain embodiments, at least one instance of R⁸ is substituted alkenyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₁₀alkenyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₈alkenyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₆alkenyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₄alkenyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₃alkenyl.

In certain embodiments, at least one instance of R⁸ is optionally substituted alkynyl. In certain embodiments, at least one instance of R⁸ is unsubstituted alkynyl. In certain embodiments, at least one instance of R⁸ is substituted alkynyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₁₀alkynyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₈alkynyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₆alkynyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₄alkynyl. In certain embodiments, at least one instance of R⁸ is optionally substituted C₂₋₃ alkynyl.

In certain embodiments, at least one instance of R⁸ is optionally substituted carbocyclyl.

In certain embodiments, at least one instance of R⁸ is optionally substituted heterocyclyl.

In certain embodiments, at least one instance of R⁸ is optionally substituted aryl.

In certain embodiments, at least one instance of R⁸ is optionally substituted heteroaryl.

In certain embodiments, q is 0. In certain embodiments, q is an integer of between 1 and 4, inclusive. In certain embodiments, q is an integer of between 1 and 3, inclusive. In certain embodiments, q is an integer of between 1 and 2, inclusive. In certain embodiments, q is 1. In certain embodiments, q is 2. In certain embodiments, q is 3. In certain embodiments, q is 4.

In certain embodiments, t is 0. In certain embodiments, t is 1. In certain embodiments, t is 2. In certain embodiments, t is 3. In certain embodiments, t is 4.

For example, in certain embodiments, wherein t is 0, the compound of Formula (V) is a compound of Formula (V-a):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, wherein t is 1, the compound of Formula (V) is a compound of Formula (V-b):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, wherein t is 2, the compound of Formula (V) is a compound of Formula (V-c):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, wherein t is 3, the compound of Formula (V) is a compound of Formula (V-d):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, wherein t is 4, the compound of Formula (V) is a compound of Formula (V-e):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, R² and R³ are independently selected from hydrogen, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl, with the proviso that R² and R³ are not both hydrogen; and R⁴ is hydrogen, an optionally substituted alkyl, or an amino protecting group.

In certain embodiments, R⁴ is hydrogen. In certain embodiments, R⁴ is optionally substituted alkyl (e.g., —CH₃, —CH₂CH₃). In certain embodiments, R⁴ is an amino protecting group as defined herein.

In certain embodiments, R² is hydrogen and R³ is independently selected from optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl. In certain embodiments, the stereochemistry of the carbon attached to R² and R³ may be (R) or (S). In certain embodiments, the stereochemistry of the carbon attached to R² and R³ is (R). In certain embodiments, the stereochemistry of the carbon attached to R² and R³ is (S).

For example, in certain embodiments wherein R² is hydrogen and the stereochemistry of the carbon attached to R² and R³ is (S), the compound of Formula (I) is a compound of Formula (VI):

or a pharmaceutically acceptable salt thereof.

In certain embodiments wherein R² is hydrogen and the stereochemistry of the carbon attached to R² and R³ is (R), the compound of Formula (I) is a compound of Formula (VII):

or a pharmaceutically acceptable salt thereof.

In certain embodiments, R² is hydrogen and R³ is optionally substituted alkyl. In certain embodiments, R² is hydrogen and R³ is a substituted alkyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₁₋₁₀ alkyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₁₋₈ alkyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₁₋₆ alkyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₁₋₄ alkyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₁₋₃ alkyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₁₋₂ alkyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₁₀ alkyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₈ alkyl. However, in certain embodiments, wherein R² is hydrogen and R³ is optionally substituted alkyl, —CH₂OR¹⁰ wherein R¹⁰ is hydrogen or acyl is specifically excluded.

In certain embodiments, R² is hydrogen and R³ is optionally substituted alkenyl. In certain embodiments, R² is hydrogen and R³ is a substituted alkenyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₁₀alkenyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₈alkenyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₆alkenyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₄alkenyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₃alkenyl.

In certain embodiments, R² is hydrogen and R³ is optionally substituted alkynyl. In certain embodiments, R² is hydrogen and R³ is a substituted alkynyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₁₀alkynyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₈alkynyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₆alkynyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₄alkynyl. In certain embodiments, R² is hydrogen and R³ is optionally substituted C₂₋₃ alkynyl.

In certain embodiments, R² is hydrogen and R³ is optionally substituted carbocyclyl.

In certain embodiments, R² is hydrogen and R³ is optionally substituted heterocyclyl.

In certain embodiments, R² is hydrogen and R³ is optionally substituted aryl.

In certain embodiments, R² is hydrogen and R³ is optionally substituted heteroaryl.

In certain embodiments, neither R² nor R³ are hydrogen, i.e., R² and R³ are independently selected from optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl. In this instance, R² and R³ are the same, or R² and R³ are different.

In certain embodiments, R² and R³ are the same and are selected from optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl. For example, in certain embodiments, R² and R³ are the same optionally substituted alkyl groups.

In certain embodiments, R² and R³ are the different and are selected from optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl. For example, in certain embodiments, R² and R³ are different optionally substituted alkyl groups.

As generally defined above, R⁵ is —OH, —SH, —NH₂, substituted hydroxyl, substituted thiol, substituted amino, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.

In certain embodiments, R⁵ is —OH. In certain embodiments, R⁵ is —SH. In certain embodiments, R⁵ is —NH₂. In certain embodiments, R⁵ is substituted hydroxyl. In certain embodiments, R⁵ is substituted thiol. In certain embodiments, R⁵ is substituted amino.

In certain embodiments, R⁵ is optionally substituted alkyl. In certain embodiments, R⁵ is unsubstituted alkyl. In certain embodiments, R⁵ is substituted alkyl. In certain embodiments, R⁵ is optionally substituted C₁₋₃₀alkyl. In certain embodiments, R⁵ is optionally substituted C₁₋₂₅alkyl. In certain embodiments, R⁵ is optionally substituted C₁₋₁₅alkyl. In certain embodiments, R⁵ is optionally substituted C₁₋₁₀alkyl. In certain embodiments, R⁵ is optionally substituted C₂₋₁₀alkyl. In certain embodiments, R⁵ is optionally substituted C₃₋₈alkyl. In certain embodiments, R⁵ is optionally substituted C₅₋₁₅alkyl.

In certain embodiments, R⁵ is optionally substituted alkenyl. In certain embodiments, R⁵ is an unsubstituted alkenyl. In certain embodiments, R⁵ is a substituted alkenyl. In certain embodiments, R⁵ is optionally substituted C₂₋₃₀ alkenyl. In certain embodiments, R⁵ is optionally substituted C₂₋₂₅ alkenyl. In certain embodiments, R⁵ is optionally substituted C₂₋₁₅ alkenyl. In certain embodiments, R⁵ is optionally substituted C₂₋₁₀ alkenyl. In certain embodiments, R⁵ is optionally substituted C₃₋₈ alkenyl. In certain embodiments, R⁵ is optionally substituted C₅₋₁₅ alkenyl.

In certain embodiments, R⁵ is a C₇₋₃₀alkyl or C₇₋₃₀alkenyl. In these instances, in certain embodiments, these groups may also collectively be referred to as “hydrocarbon tails.” Hydrocarbon tails can be saturated and unsaturated, depending on whether or not the hydrocarbon tail comprises double bonds. The hydrocarbon tail can also comprise different lengths, often categorized as medium (i.e., with tails between 7-12 carbons, e.g., C₇₋₁₂ alkyl or C₇₋₁₂ alkenyl), long (i.e., with tails greater than 12 carbons and up to 22 carbons, e.g., C₁₃₋₂₂ alkyl or C₁₃₋₂₂ alkenyl), or very long (i.e., with tails greater than 22 carbons, e.g., C₂₃₋₃₀ alkyl or C₂₃₋₃₀ alkenyl).

Exemplary unsaturated hydrocarbon tails include, but are not limited to:

-   Myristoleic —(CH₂)₇CH═CH(CH₂)₃CH₃, -   Palmitoliec —(CH₂)₇CH═CH(CH₂)₅CH₃, -   Sapienic —(CH₂)₄CH═CH(CH₂)₈CH₃, -   Oleic —(CH₂)₇CH═CH(CH₂)₇CH₃, -   Linoleic —(CH₂)₇CH═CHCH₂CH═CH(CH₂)₄CH₃, -   α-Linolenic —(CH₂)₇CH═CHCH₂CH═CHCH₂CH═CHCH₂CH₃, -   Arachinodonic —(CH₂)₃CH═CHCH₂CH═CHCH₂CH═CHCH₂CH═CH(CH₂)₄CH₃, -   Eicosapentaenoic —(CH₂)₃CH═CHCH₂CH═CHCH₂CH═CHCH₂CH═CHCH₂CH═CHCH₂CH₃, -   Erucic —(CH₂)₁₁CH═CH(CH₂)₇CH₃, and -   Docosahexaenoic     —(CH₂)₂CH═CHCH₂CH═CHCH₂CH═CHCH₂CH═CHCH₂CH═CHCH₂CH═CH—CH₂CH₃.

Exemplary saturated hydrocarbon tails include, but are not limited to:

-   -   Lauric —(CH₂)₁₀CH₃,     -   Myristic —(CH₂)₁₂CH₃,     -   Palmitic —(CH₂)₁₄CH₃,     -   Stearic —(CH₂)₁₆CH₃,     -   Arachidic —(CH₂)₁₈CH₃,     -   Behenic —(CH₂)₂₀CH₃,     -   Lignoceric —(CH₂)₂₂CH₃, and     -   Cerotic —(CH₂)₂₄CH₃.

In certain embodiments, R⁵ is an optionally substituted alkenyl group of formula (a):

wherein:

x is an integer between 1 and 10, inclusive;

R^(10a) and R^(10b) are independently hydrogen or optionally substituted alkyl; and

R⁹ is hydrogen, halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.

In certain embodiments, x is an integer between 1 and 8, inclusive. In certain embodiments, x is an integer between 1 and 6, inclusive. In certain embodiments, x is an integer between 1 and 5, inclusive. In certain embodiments, x is an integer between 1 and 4, inclusive. In certain embodiments, x is an integer between 1 and 3, inclusive. In certain embodiments, x is an integer between 1 and 2, inclusive. In certain embodiments, x is 1. In certain embodiments, x is 2. In certain embodiments, x is 3. In certain embodiments, x is 4. In certain embodiments, x is 5.

In certain embodiments, R^(10a) and R^(10b) are both hydrogen. In certain embodiments, R^(10a) and R^(10b) are independently selected from hydrogen and —CH₃.

In certain embodiments, R⁹ is selected from acyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl.

In certain embodiments, R⁹ is a acyl, as defined herein.

In certain embodiments, R⁹ is optionally substituted alkyl (e.g., —CH₃, —CH₂CH₃, —CH₂CH₂CH₃, —CH₂CH₂CH₂CH₃).

In certain embodiments, the alkenyl group of Formula (a) is selected from:

In certain embodiments, R⁵ is optionally substituted alkynyl. In certain embodiments, R⁵ is an unsubstituted alkynyl. In certain embodiments, R⁵ is a substituted alkynyl. In certain embodiments, R⁵ is optionally substituted C₂₋₃₀ alkynyl. In certain embodiments, R⁵ is optionally substituted C₂₋₂₅ alkynyl. In certain embodiments, R⁵ is optionally substituted C₂₋₁₅ alkynyl. In certain embodiments, R⁵ is optionally substituted C₂₋₁₀ alkynyl. In certain embodiments, R⁵ is optionally substituted C₃₋₈ alkynyl. In certain embodiments, R⁵ is optionally substituted C₅₋₁₅ alkynyl.

As generally described above, R¹¹ is hydrogen, —OH, —SH, —NH₂, substituted hydroxyl, substituted thiol, substituted amino, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl. In certain embodiments, R¹¹ is hydrogen. In certain embodiments, R¹¹ is optionally substituted alkyl. In certain embodiments, R¹¹ is C₁₋₃ optionally substituted alkyl, e.g., —CH₃, —CF₃, —CH₂CH₃, or —CH(CH₃)₂. In certain embodiments, R¹¹ is —CH₃.

As generally described above, R¹² is hydrogen, —OH, —SH, —NH₂, substituted hydroxyl, substituted thiol, substituted amino, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl. In certain embodiments, R¹² is hydrogen. In certain embodiments, R¹² is optionally substituted alkyl. In certain embodiments, R¹² is C₁₋₃ optionally substituted alkyl, e.g., —CH₃, —CF₃, —CH₂CH₃, or —CH(CH₃)₂. In certain embodiments, R¹² is —CH₃.

As generally described above, each instance of R⁶ is independently selected from halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, and optionally substituted heteroaryl; and m is 0 or an integer of between 1 and 5, inclusive.

In certain embodiments, m is 0. In certain embodiments, m is an integer of between 1 and 5, inclusive. In certain embodiments, m is an integer of between 1 and 4, inclusive. In certain embodiments, m is an integer of between 1 and 3, inclusive. In certain embodiments, m is an integer of between 1 and 2, inclusive. In certain embodiments, m is 1, i.e., to provide a monosubstituted phenyl. In certain embodiments, m is 2, i.e., to provide a disubstituted phenyl. In certain embodiments, m is 3, i.e., to provide a trisubstituted phenyl. In certain embodiments, m is 4, i.e., to provide a tetrasubstituted phenyl. In certain embodiments, m is 5, i.e., to provide a pentasubstituted phenyl.

In certain preferred embodiments, m is 1 or 2 to provide a monosubstituted or disubstituted phenyl. In this instance, all possible positional mono- and di-substituted isomers are contemplated herein, i.e.:

For example, in certain embodiments, m is 1, i.e., to provide a monosubstituted phenyl. In this instance, R⁶ may be an ortho-, meta- or para-substituent relative to the point of attachment to the parent molecule. In certain embodiments, R⁶ is an ortho-substituent. In certain embodiments, R⁶ is a meta-substituent. In certain embodiments, R⁶ is a para-substituent.

In certain embodiments, m is 2, i.e., to provide a disubstituted phenyl. In this instance, the two R⁶ substituents are 1,2-substituents, 1,3-substituents, 1,4-substituents, 1,5-substituents, 2,3-substituents, or 2,4-substituents, relative to the point of attachment to the parent molecule. In certain embodiments, the two R⁶ substituents are1,2-substituents. In certain embodiments, the two R⁶ substituents are 1,3-substituents. In certain embodiments, the two R⁶ substituents are 1,4-substituents. In certain embodiments, the two R⁶ substituents are 1,5-substituents. In certain embodiments, the two R⁶ substituents are 2,3-substituents. In certain embodiments, the two R⁶ substituents are 2,4-substituents.

In certain embodiments, each instance of R⁶ is independently selected from halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, and boronyl. In certain embodiments, each instance of R⁶ is independently selected from halogen, —OH, —SH, —NH₂, —SO₂H, —SO₃H. In certain embodiments, each instance of R⁶ is independently selected from halogen, —OH, or —NH₂.

In certain embodiments, each instance of R⁶ is halogen, e.g., fluoro (—F), chloro (—Cl), bromo (—Br), or iodo (—I). In certain embodiments, each instance of R⁶ is fluoro. In certain embodiments, m is 1 and R⁶ is fluoro. In certain embodiments, m is 1 and R⁶ is a meta fluoro substituent. In certain embodiments, m is 2 and each R⁶ is fluoro. In certain embodiments, m is 2 and the two R⁶ groups are 2,4-fluoro substituents.

In certain embodiments, each instance of R⁶ is —OH. In certain embodiments, m is 1 and R⁶ is —OH. In certain embodiments, m is 1 and R⁶ is —OH. In certain embodiments, m is 1 and R⁶ is a meta —OH substituent.

In certain embodiments, each instance of R⁶ is —NH₂. In certain embodiments, m is 1 and R⁶ is —NH₂. In certain embodiments, m is 1 and R⁶ is a meta —NH₂ substituent.

For example, in certain embodiments of Formula (I), wherein m is 1 or 2, provided is a compound of Formula (I-b) or (I-c):

or a pharmaceutically acceptable salt thereof.

However, in certain embodiments, the compound of Formula (I) is not Enopeptin A, Enopeptin B, A54556A, A54556B, or ADEP4, or salt thereof, as depicted in FIG. 1. In certain embodiments, the compound of Formula (I) is not a compound or salt thereof as depicted in WO2003/024996.

Exemplary compounds of Formula (I) include, but are not limited to:

and pharmaceutically acceptable salts thereof.

Methods of Synthesis

The present invention also provides methods of preparing compounds of Formula (I). The method is a convergent approach and employs various deprotections and peptide coupling throughout the synthesis. Deprotecting conditions are well known in the art (see, e.g., Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley & Sons, 1999). Reagents and conditions for peptide coupling (e.g., uronium, immonium, carbodiimide, imidazolium, organophosphorous coupling reagents) are also well known in the art; see, e.g., Han and Kim, Tetrahedron (2004) 60:2447-2467.

For example, in one aspect, provided is a method of preparing a compound of Formula (C):

or salt thereof; comprising coupling a compound of Formula (A), or salt thereof, with a compound of Formula (B), or salt thereof:

wherein PG¹ and PG⁷ are amino protecting groups, as defined herein; and PG⁸ is an oxygen protecting group, as defined herein.

In certain embodiments, PG¹ is a -Boc group. In certain embodiments, PG⁷ is a Cbz group. In certain embodiments, PG⁸ is a 2-hydroxy-1-phenylethanone (HPE) group.

In certain embodiments, the method further comprises deprotecting the compound of Formula (C), or salt thereof, to provide a compound of Formula (E):

or salt thereof.

In certain embodiments, the method further comprises cyclizing the compound of Formula (E), or salt thereof, to provide a compound of Formula (F):

or salt thereof.

The cyclization reaction is an intramolecular peptide coupling reaction.

In certain embodiments, the method further comprises deprotecting the compound of Formula (F), or salt thereof, to provide a compound of Formula (G):

or salt thereof.

In certain embodiments, the step of deprotecting (removal of PG⁷) involves hydrogenation, or use of hydrogen transfer conditions.

In certain embodiments, the method further comprises coupling the compound of Formula (G), or salt thereof, with a compound of Formula (H):

or salt thereof; to provide a compound of Formula (I) or salt thereof.

In certain embodiments, the compound of Formula (A), or salt thereof, is prepared by a Ugi 4-component reaction or a Joulie-Ugi 3-component reaction, i.e., as depicted in FIG. 3, followed by deprotection, wherein PG² is an oxygen protecting group.

In certain embodiments, PG² is a methyl group. In certain embodiments, the step of deprotecting (removal of PG²) involves basic hydrolysis (e.g., use of NaOH, LiOH).

Pharmaceutical Compositions

In certain embodiments, the present invention provides a pharmaceutical composition comprising a compound of the present invention, e.g., a compound of Formula (I) or a pharmaceutically acceptable salt thereof, and, optionally, a pharmaceutically acceptable excipient. In certain embodiments, the compound of the present invention is provided in an effective amount in the pharmaceutical composition, e.g., a therapeutically effective amount and/or a prophylactically effective amount, depending upon the intended method of treatment.

Pharmaceutically acceptable excipients include any and all solvents, diluents or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. General considerations in formulation and/or manufacture of pharmaceutical compositions agents can be found, for example, in Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980), and Remington: The Science and Practice of Pharmacy, 21st Edition (Lippincott Williams & Wilkins, 2005).

Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include the steps of bringing the compound of the present invention (the “active ingredient”) into association with a carrier and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.

Pharmaceutical compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses. As used herein, a “unit dose” is discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient. The amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.

Relative amounts of the active ingredient, the pharmaceutically acceptable excipient, and/or any additional ingredients in a pharmaceutical composition of the invention will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered. By way of example, the composition may comprise between 0.1% and 100% (w/w) active ingredient.

Pharmaceutically acceptable excipients used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.

Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, etc., and combinations thereof.

Exemplary granulating and/or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose and wood products, natural sponge, cation-exchange resins, calcium carbonate, silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, quaternary ammonium compounds, etc., and combinations thereof.

Exemplary surface active agents and/or emulsifiers include natural emulsifiers (e.g. acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays (e.g. bentonite [aluminum silicate] and Veegum [magnesium aluminum silicate]), long chain amino acid derivatives, high molecular weight alcohols (e.g. stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers (e.g. carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g. carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters (e.g. polyoxyethylene sorbitan monolaurate (Tween 20), polyoxyethylene sorbitan (Tween 60), polyoxyethylene sorbitan monooleate (Tween 80), sorbitan monopalmitate (Span 40), sorbitan monostearate (Span 60), sorbitan tristearate (Span 65), glyceryl monooleate, sorbitan monooleate (Span 80)), polyoxyethylene esters (e.g. polyoxyethylene monostearate (Myrj 45), polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil, polyoxymethylene stearate, and Solutol), sucrose fatty acid esters, polyethylene glycol fatty acid esters (e.g. Cremophor), polyoxyethylene ethers, (e.g. polyoxyethylene lauryl ether (Brij 30)), poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic F-68, Poloxamer P188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, etc. and/or combinations thereof.

Exemplary binding agents include starch (e.g. cornstarch and starch paste), gelatin, sugars (e.g. sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums (e.g. acacia, sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, microcrystalline cellulose, cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate (Veegum), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, etc., and/or combinations thereof.

Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, alcohol preservatives, acidic preservatives, and other preservatives.

Exemplary antioxidants include alpha tocopherol, ascorbic acid, acorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium metabisulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.

Exemplary chelating agents include ethylenediaminetetraacetic acid (EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof. Exemplary antimicrobial preservatives include benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.

Exemplary antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium benzoate, sodium propionate, and sorbic acid.

Exemplary alcohol preservatives include ethanol, polyethylene glycol, phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.

Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.

Other preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant Plus, Phenonip, methylparaben, Germall 115, Germaben II, Neolone, Kathon, and Euxyl. In certain embodiments, the preservative is an anti-oxidant. In other embodiments, the preservative is a chelating agent.

Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D-gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium acetate, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline, Ringer's solution, ethyl alcohol, etc., and combinations thereof.

Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, etc., and combinations thereof.

Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea buckthorn, sesame, shea butter, silicone, soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, and wheat germ oils. Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and combinations thereof.

Liquid dosage forms for oral and parenteral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredients, the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the conjugates of the invention are mixed with solubilizing agents such as Cremophor, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and combinations thereof.

Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation can be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This can be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.

Compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing the conjugates of this invention with suitable nonirritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.

Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may comprise buffering agents.

Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes. Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.

The active ingredients can be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active ingredient can be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may comprise buffering agents. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes.

Dosage forms for topical and/or transdermal administration of a compound of this invention may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches. Generally, the active ingredient is admixed under sterile conditions with a pharmaceutically acceptable carrier and/or any needed preservatives and/or buffers as can be required. Additionally, the present invention contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of an active ingredient to the body. Such dosage forms can be prepared, for example, by dissolving and/or dispensing the active ingredient in the proper medium. Alternatively or additionally, the rate can be controlled by either providing a rate controlling membrane and/or by dispersing the active ingredient in a polymer matrix and/or gel.

Suitable devices for use in delivering intradermal pharmaceutical compositions described herein include short needle devices such as those described in U.S. Pat. Nos. 4,886,499; 5,190,521; 5,328,483; 5,527,288; 4,270,537; 5,015,235; 5,141,496; and 5,417,662. Intradermal compositions can be administered by devices which limit the effective penetration length of a needle into the skin, such as those described in PCT publication WO 99/34850 and functional equivalents thereof. Jet injection devices which deliver liquid vaccines to the dermis via a liquid jet injector and/or via a needle which pierces the stratum corneum and produces a jet which reaches the dermis are suitable. Jet injection devices are described, for example, in U.S. Pat. Nos. 5,480,381; 5,599,302; 5,334,144; 5,993,412; 5,649,912; 5,569,189; 5,704,911; 5,383,851; 5,893,397; 5,466,220; 5,339,163; 5,312,335; 5,503,627; 5,064,413; 5,520,639; 4,596,556; 4,790,824; 4,941,880; 4,940,460; and PCT publications WO 97/37705 and WO 97/13537. Ballistic powder/particle delivery devices which use compressed gas to accelerate vaccine in powder form through the outer layers of the skin to the dermis are suitable. Alternatively or additionally, conventional syringes can be used in the classical mantoux method of intradermal administration.

Formulations suitable for topical administration include, but are not limited to, liquid and/or semi liquid preparations such as liniments, lotions, oil in water and/or water in oil emulsions such as creams, ointments and/or pastes, and/or solutions and/or suspensions. Topically-administrable formulations may, for example, comprise from about 1% to about 10% (w/w) active ingredient, although the concentration of the active ingredient can be as high as the solubility limit of the active ingredient in the solvent. Formulations for topical administration may further comprise one or more of the additional ingredients described herein.

A pharmaceutical composition of the invention can be prepared, packaged, and/or sold in a formulation suitable for pulmonary administration via the buccal cavity. Such a formulation may comprise dry particles which comprise the active ingredient and which have a diameter in the range from about 0.5 to about 7 nanometers or from about 1 to about 6 nanometers. Such compositions are conveniently in the form of dry powders for administration using a device comprising a dry powder reservoir to which a stream of propellant can be directed to disperse the powder and/or using a self propelling solvent/powder dispensing container such as a device comprising the active ingredient dissolved and/or suspended in a low-boiling propellant in a sealed container. Such powders comprise particles wherein at least 98% of the particles by weight have a diameter greater than 0.5 nanometers and at least 95% of the particles by number have a diameter less than 7 nanometers. Alternatively, at least 95% of the particles by weight have a diameter greater than 1 nanometer and at least 90% of the particles by number have a diameter less than 6 nanometers. Dry powder compositions may include a solid fine powder diluent such as sugar and are conveniently provided in a unit dose form.

Low boiling propellants generally include liquid propellants having a boiling point of below 65° F. at atmospheric pressure. Generally the propellant may constitute 50 to 99.9% (w/w) of the composition, and the active ingredient may constitute 0.1 to 20% (w/w) of the composition. The propellant may further comprise additional ingredients such as a liquid non-ionic and/or solid anionic surfactant and/or a solid diluent (which may have a particle size of the same order as particles comprising the active ingredient).

Pharmaceutical compositions of the invention formulated for pulmonary delivery may provide the active ingredient in the form of droplets of a solution and/or suspension. Such formulations can be prepared, packaged, and/or sold as aqueous and/or dilute alcoholic solutions and/or suspensions, optionally sterile, comprising the active ingredient, and may conveniently be administered using any nebulization and/or atomization device. Such formulations may further comprise one or more additional ingredients including, but not limited to, a flavoring agent such as saccharin sodium, a volatile oil, a buffering agent, a surface active agent, and/or a preservative such as methylhydroxybenzoate. The droplets provided by this route of administration may have an average diameter in the range from about 0.1 to about 200 nanometers.

Formulations described herein as being useful for pulmonary delivery are useful for intranasal delivery of a pharmaceutical composition of the invention. Another formulation suitable for intranasal administration is a coarse powder comprising the active ingredient and having an average particle from about 0.2 to 500 micrometers. Such a formulation is administered. by rapid inhalation through the nasal passage from a container of the powder held close to the nares.

Formulations for nasal administration may, for example, comprise from about as little as 0.1% (w/w) and as much as 100% (w/w) of the active ingredient, and may comprise one or more of the additional ingredients described herein. A pharmaceutical composition of the invention can be prepared, packaged, and/or sold in a formulation for buccal administration. Such formulations may, for example, be in the form of tablets and/or lozenges made using conventional methods, and may contain, for example, 0.1 to 20% (w/w) active ingredient, the balance comprising an orally dissolvable and/or degradable composition and, optionally, one or more of the additional ingredients described herein. Alternately, formulations for buccal administration may comprise a powder and/or an aerosolized and/or atomized solution and/or suspension comprising the active ingredient. Such powdered, aerosolized, and/or aerosolized formulations, when dispersed, may have an average particle and/or droplet size in the range from about 0.1 to about 200 nanometers, and may further comprise one or more of the additional ingredients described herein.

A pharmaceutical composition of the invention can be prepared, packaged, and/or sold in a formulation for ophthalmic administration. Such formulations may, for example, be in the form of eye drops including, for example, a 0.1/1.0% (w/w) solution and/or suspension of the active ingredient in an aqueous or oily liquid carrier. Such drops may further comprise buffering agents, salts, and/or one or more other of the additional ingredients described herein. Other opthalmically-administrable formulations which are useful include those which comprise the active ingredient in microcrystalline form and/or in a liposomal preparation. Ear drops and/or eye drops are contemplated as being within the scope of this invention.

Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation.

Still further encompassed by the invention are kits (e.g., pharmaceutical packs). The kits provided may comprise an inventive pharmaceutical composition or compound and a container (e.g., a vial, ampule, bottle, syringe, and/or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a pharmaceutical excipient for dilution or suspension of an inventive pharmaceutical composition or compound. In some embodiments, the inventive pharmaceutical composition or compound provided in the container and the second container are combined to form one unit dosage form.

Optionally, a single container may comprise one or more compartments for containing an inventive pharmaceutical composition or compound, and/or a pharmaceutically acceptable excipient for suspension or dilution. In some embodiments, a single container can be appropriate for modification such that the container may receive a physical modification so as to allow combination of compartments and/or components of individual compartments. For example, a foil or plastic bag may comprise two or more compartments separated by a perforated seal which can be broken so as to allow combination of contents of two individual compartments once the signal to break the seal is generated. A kit may thus comprise such multi-compartment containers providing an inventive pharmaceutical composition or compound and one or more pharmaceutically acceptable excipients.

Optionally, instructions for use are additionally provided in such kits of the invention. Such instructions may provide, generally, for example, instructions for dosage and administration. In other embodiments, instructions may further provide additional detail relating to specialized instructions for particular containers and/or systems for administration. Still further, instructions may provide specialized instructions for use in conjunction and/or in combination with an additional therapeutic agent.

Methods of Use and Treatment

The present invention also provides methods of using compounds of the present invention, e.g., a compound of Formula (I) or a pharmaceutically acceptable salt thereof, as described herein.

For example, in one aspect, provided are methods of treating a microbial infection in a subject, comprising administering an effective amount of a compound of the present invention.

In another aspect, provided is a method of treating microbial virulence. Such a method can be conducted by contacting the compound of the present invention, in vivo (i.e., by administration to a subject) or in vitro (e.g., upon contact with the microorganism in a cell culture).

For example, in certain embodiments, provided is a method of treating microbial virulence comprising contacting an effective amount of the compound of the present invention with a microorganism. In certain embodiments, provided is an in vitro method of treating microbial virulence comprising contacting an effective amount of the compound of the present invention with a microorganism in a cell culture. In certain embodiments, provided is an in vivo method of treating microbial virulence comprising administering an effective amount of the compound of the present invention to a subject with a microbial infection. In certain embodiments, the compound of the present invention blocks virulence factor production. In certain embodiments, the microbial virulence is bacterial virulence, and the microorganism is a bacterium.

As used herein, a “microbial infection” refers to an infection with a microorganism, such as a fungus, bacteria or virus. In certain embodiments, the microbial infection is an infection with a fungus, i.e., a fungal infection. In certain embodiments, the microbial infection is an infection with a virus, i.e., a viral infection. In certain embodiments, the microbial infection is an infection with a bacteria, i.e., a bacterial infection. Various microbial infections include, but are not limited to, skin infections, GI infections, urinary tract infections, genito-urinary infections, sepsis, blood infections, and systemic infections.

In certain embodiments, the microbial infection is an infection with a bacteria, i.e., a bacterial infection. In certain embodiments, the compounds of the invention exhibit anti-bacterial activity. For example, in certain embodiments, the compound has a mean inhibitory concentration, with respect to a particular bacterium, of less than 50 μg/mL, preferably less than 25 μg/mL, more preferably less than 5 μg/mL, and most preferably less than 1 μg/mL.

Exemplary bacterial infections include, but are not limited to, infections with a gram positive bacteria (e.g., of the phylum Actinobacteria, phylum Firmicutes, or phylum Tenericutes); gram negative bacteria (e.g., of the phylum Aquificae, phylum Deinococcus-Thermus, phylum Fibrobacteres/Chlorobi/Bacteroidetes (FCB), phylum Fusobacteria, phylum Gemmatimonadest, phylum Ntrospirae, phylum Planctomycetes/Verrucomicrobia/Chlamydiae (PVC), phylum Proteobacteria, phylum Spirochaetes, or phylum Synergistetes); or other bacteria (e.g., of the phylum Acidobacteria, phylum Chlroflexi, phylum Chrystiogenetes, phylum Cyanobacteria, phylum Deferrubacteres, phylum Dictyoglomi, phylum Thermodesulfobacteria, or phylum Thennotogae).

In certain embodiments, the bacterial infection is an infection with a gram positive bacteria. In certain embodiments, the gram positive bacteria is a bacteria of the phylum Firmicutes. In certain embodiments, the bacteria is a member of the phylum Firmicutes and the genus Enterococcus, i.e., the bacterial infection is an Enterococcus infection. Exemplary Enterococci bacteria include, but are not limited to, E. avium, E. durans, E. faecalis, E. faecium, E. gallinarum, E. solitarius, E. casseliflavus, and E. raffinosus. In certain embodiments, the Enterococcus infection is an E. faecalis infection. In certain embodiments, the Enterococcus infection is an E. faecium infection.

In certain embodiments, the bacteria is a member of the phylum Firmicutes and the genus Staphylococcus, i.e., the bacterial infection is a Staphylococcus infection. Exemplary Staphylococci bacteria include, but are not limited to, S. arlettae, S. aureus, S. auricularis, S. capitis, S. caprae, S. carnous, S. chromogenes, S. cohii, S. condimenti, S. croceolyticus, S. delphini, S. devriesei, S. epidermis, S. equorum, S. felis, S. fluroettii, S. gallinarum, S. haemolyticus, S. hominis, S. hyicus, S. intermedius, S. kloosii, S. leei, S. lenus, S. lugdunesis, S. lutrae, S. lyticans, S. massiliensis, S. microti, S. muscae, S. nepalensis, S. pasteuri, S. penttenkoferi, S. piscifermentans, S. psuedointermedius, S. psudolugdensis, S. pulvereri, S. rostri, S. saccharolyticus, S. saprophyticus, S. schleiferi, S. sciuri, S. simiae, S. simulans, S. stepanovicii, S. succinus, S. vitulinus, S. warneri, and S. xylosus. In certain embodiments, the Staphylococcus infection is an S. aureus infection. In certain embodiments, the Staphylococcus infection is an S. epidermis infection.

In certain embodiments, the bacterial infection is resistant to other antibiotic therapy. For example, in certain embodiments, the bacterial infection is vancomycin resistant (VR). In certain embodiments, the bacterial infection is a vancomycin-resistant E. faecalis infection. In certain embodiments, the bacterial infection is a vancomycin-resistant E. faecium infection. In certain embodiments, the bacterial infection is a methicillin-resistant (MR). In certain embodiments, the bacterial infection is a methicillin-resistant S. aureus (MRSA) infection.

In yet another aspect, provided is a method of treating bacterial infection and/or virulence including the treatment of bacteria or infection caused by bacteria that are resistent to other treatments, are multi-drug tolerant or resistent and/or that neither grow nor die in the presence of or as a result of other treatments. Such a method can be conducted in vivo (i.e., by administration to a subject) or in vitro (e.g., upon contact with bacteria in a cell culture). For example, in certain embodiments, provided is a method of treating bacterial virulence comprising administering an effective amount of a compound of the present invention e.g., a compound of Formula (I) or a pharmaceutically acceptable salt thereof, to a subject with a bacterial infection. In certain embodiments, the compound blocks virulence factor production.

In another aspect, the compounds of the present invention inhibit the growth of or kill rapidly dividing cells such as stimulated inflammatory cells. Thus, the present invention also contemplates the treatment of a disease, disorder, or condition associated with abnormal cellular proliferation, such as cancer, autoimmune diseases, inflammatory diseases, and diabetic retinopathy.

Thus, in one aspect, provided is a method of treating cancer comprising administering an effective amount of the compound of the present invention or pharmaceutically acceptable salt thereof to a subject.

In another aspect, provided is a method of treating an autoimmune disease comprising administering an effective amount of the compound of the present invention or pharmaceutically acceptable salt thereof to a subject.

In yet another aspect, provided is a method of treating an inflammatory disease comprising administering the compound of the present invention or pharmaceutically acceptable salt thereof to a subject.

In yet another aspect, provided is a method of treating diabetic retinopathy comprising administering an effective amount of the compound of the present invention or pharmaceutically acceptable salt thereof to a subject.

Compounds provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disease, disorder, or condition being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.

The compounds and compositions provided herein can be administered by any route, including enteral (e.g., oral), parenteral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation; and/or as an oral spray, nasal spray, and/or aerosol. Specifically contemplated routes are oral administration, intravenous administration (e.g., systemic intravenous injection), regional administration via blood and/or lymph supply, and/or direct administration to an affected site. In general the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g., its stability in the environment of the gastrointestinal tract), the condition of the subject (e.g., whether the subject is able to tolerate oral administration), etc.

The exact amount of a compound required to achieve an effective amount will vary from subject to subject, depending, for example, on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound(s), mode of administration, and the like. The desired dosage can be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage can be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).

In certain embodiments, an effective amount of a compound for administration one or more times a day to a 70 kg adult human may comprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000 mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg, about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1 mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about 1000 mg, or about 100 mg to about 1000 mg, of a compound per unit dosage form.

In certain embodiments, the compounds of the invention may be administered orally or parenterally at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kg to about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, and more preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.

It will be appreciated that dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult. The amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.

It will be also appreciated that a compound or composition, as described herein, can be administered in combination with one or more additional therapeutically active agents. The compounds or compositions can be administered in combination with additional therapeutically active agents that improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body. It will also be appreciated that the therapy employed may achieve a desired effect for the same disorder, and/or it may achieve different effects.

The compound or composition can be administered concurrently with, prior to, or subsequent to, one or more additional therapeutically active agents. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent. In will further be appreciated that the additional therapeutically active agent utilized in this combination can be administered together in a single composition or administered separately in different compositions. The particular combination to employ in a regimen will take into account compatibility of the inventive compound with the additional therapeutically active agent and/or the desired therapeutic effect to be achieved. In general, it is expected that additional therapeutically active agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.

Exemplary additional therapeutically active agents include, but are not limited to, antibiotics, anti-viral agents, anesthetics, anti-coagulants, inhibitors of an enzyme, steroidal agents, steroidal or non-steroidal anti-inflammatory agents, antihistamine, immunosuppressant agents, antigens, vaccines, antibodies, decongestant, sedatives, opioids, pain-relieving agents, analgesics, anti-pyretics, hormones, and prostaglandins, etc. Therapeutically active agents include small organic molecules such as drug compounds (e.g., compounds approved by the US Food and Drug Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins and cells.

In certain embodiments, the additional therapeutically agent is an antibiotic. Exemplary antibiotics include, but are not limited to, penicillins (e.g., penicillin, amoxicillin), cephalosporins (e.g., cephalexin), macrolides (e.g., erythromycin, clarithormycin, azithromycin, troleandomycin), fluoroquinolones (e.g., ciprofloxacin, levofloxacin, ofloxacin), sulfonamides (e.g., co-trimoxazole, trimethoprim), tetracyclines (e.g., tetracycline, chlortetracycline, oxytetracycline, demeclocycline, methacycline, sancycline, doxycline, aureomycin, terramycin, minocycline, 6-deoxytetracycline, lymecycline, meclocycline, methacycline, rolitetracycline, and glycylcycline antibiotics (e.g., tigecycline)), aminoglycosides (e.g., gentamicin, tobramycin, paromomycin), aminocyclitol (e.g., spectinomycin), chloramphenicol, sparsomycin, quinupristin/dalfoprisin (Syndercid™),

In certain embodiments, the antibiotic is a ribosome-targeting antibiotic.

Antibiotics target ribosomes at distinct locations within functionally relevant sites. They exert their inhibitory action by diverse modes, including competing with substrate binding, interfering with ribosomal dynamics, minimizing ribosomal mobility, facilitating miscoding, hampering the progression of the mRNA chain, and blocking the nascent protein exit tunnel. Examples of antibiotics that reveal novel ribosomal properties or enforced otherwise observed findings include the following: decoding (paromomycin); mRNA progression (spectinomycin); A-site binding to the small (tetracycline antibiotic) and the large (chloramphenicol) subunits; PTC mobility (sparsomycin); tRNA rotatory motion (quinupristin/dalfoprisin), and tunnel gating (troleandomycin); see Yonath, Annu. Rev. Biochem. (2005) 74:649-679.

In certain embodiments, the ribosome-targeting antibiotic is a tetracycline antibiotic. Exemplary tetracycline antibiotics include, but are not limited to, tetracycline, chlortetracycline, oxytetracycline, demeclocycline, methacycline, sancycline, doxycline, aureomycin, terramycin, minocycline, 6-deoxytetracycline, lymecycline, meclocycline, methacycline, rolitetracycline, and glycylcycline antibiotics (e.g., tigecycline).

EXAMPLES

In order that the invention described herein may be more fully understood, the following examples are set forth. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting this invention in any manner.

Example 1 Diversity-Oriented Synthesis of Cyclic Acyldepsipeptides

In an effort to improve the pharmacological properties of the enopeptins, a research group at Bayer Pharmaceuticals carried out an intensive structure-activity-relationship (SAR) study of the enopeptins (see, e.g., Hinzen et al., Chem Med Chem (2006) 1:689; U.S. 20050107288). Their medicinal chemistry program was guided by the observation that the conformation of the peptidolactone core structure was constrained by two transannular hydrogen bonds to the phenylalanine moiety of the side chain. On this basis, it was anticipated that replacing the constituents of the peptidolactone with conformationally restricted amino acids would yield enopeptin derivatives with improved antibacterial activity. Although most changes in the peptidolactone decreased antibacterial activity, replacement of N-methylalanine with a rigid pipecolate moiety yielded a more potent analogue. Presumably, rigidification of the peptidolactone lowers the entropic cost of binding to the ClpP core. The stability and antibacterial activity of these rigidified enopeptin analogs were further enhanced by replacement of the exocyclic phenylalanine with 3,5-difluorophenylalanine and by substitution of the polyunsaturated side chain with a 2-heptenoyl moiety. The optimized enopeptin derivative, known as acyl depsipeptide 4 (ADEP 4), exhibited remarkable activity both in vitro and in vivo (FIG. 1). As was the case for the parent enopeptins, no cross-resistance to ADEP 4 was observed and the compound was active against multidrug resistant pathogens. The minimum inhibitory concentration (MIC) and in vivo antibacterial activity of ADEP 4 equaled or even surpassed that of established antibacterial drugs. Remarkably, mice infected with a lethal innocula of Enterococcus faecalis had a 100% survival rate when treated with a single dose of ADEP 4 at 0.5 mg/kg. The development of ADEP 4 clearly indicates the power of medicinal chemistry in enhancing the properties of natural products.

Given the promise of ADEP 4 as an antibacterial drug, we sought to develop an efficient synthetic route to the peptidolactone core of this molecule that also allowed for the preparation of other conformationally constricted enopeptin derivatives. In the interest of expediency, we planned to capitalize on the convergent scheme used in the syntheses of ADEP 4 (and of enopeptins A and B) in which a tripeptide fragment and an ester fragment are coupled, cyclized and acylated (FIG. 2) (see, e.g., Schmidt et al., Angew. Chem. Int. Ed. Engl. (1997) 36:1110). Our objective was to develop an efficient and diversity-oriented synthesis of the tripeptide precursor of ADEP 4 (Ala-Pip-Pro). The published chemical synthesis of this tripeptide fragment uses standard peptide chemistry and as such is limited by three distinct steps for removal of protecting groups, a challenging acylation of a secondary amide (pipecolamide), and a dependence on commercially-available amino acids. An ideal synthesis of the tripeptide would be higher yielding, greater in atom economy, and enable facile exchange of ADEP 4′s pipecolate with other conformationally rigid amino acids for SAR studies. We hypothesized that the tripeptide precursor of ADEP 4 and other conformationally restricted tripeptides could be prepared in a single step via isocyanide-based multicomponent reactions (FIG. 3) (see, e.g., Dömling et al., Angew. Chem., Int. Ed. (2000) 39:3168; Dömling, Chem. Rev. (2006) 106:17). Pipecolate containing tripeptides reminiscent of the ADEP 4 tripeptide precursor can be prepared from six-membered cyclic imines, N-Boc-proline, and an isocyanide derived from alanine methyl ester in a Joullié-Ugi three-component reaction (Joullié-Ugi 3CR) (see, e.g., Nutt et al., J. Am. Chem. Soc. (1982) 104:5852; Nenajdenko et al., Tetrahedron. (2006) 62:5922). Similarly, peptides with conformationally restricted N-methyl, α,α-disubstituted amino acids can be prepared with an Ugi four-component reaction (Ugi 4CR) from methylamine, various ketones, N-Boc-proline, and an isocyanide derived from alanine methyl ester (see, e.g., Simila et al., Tetrahedron Lett. (2008) 49:4501).

This Example describes a diversity-oriented synthesis of the tripeptide fragment featuring isocyanide-based multicomponent reactions that enabled the preparation of eight enopeptin derivatives. The antibacterial activity of these analogues against clinical isolates of methicillin-sensitive S. aureus (MSSA), methicillin-resistant S. aureus (MRSA), vancomycin-susceptible E. faecalis and vancomycin-resistant E. faecium (VRE) was systematically assessed. Additionally, we report for the first time the minimum bactericidal concentration (MBC) of any enopeptin derivatives. It is noteworthy that a novel ADEP 4 derivative with 4-methyl pipecolate in place of pipecolate has considerably enhanced activity against pathogenic Enterococci.

Synthesis and Elaboration of the ADEP 4 Peptidolactone Core Structure

Our initial objective was to prepare 10a, a more synthetically accessible analogue of ADEP 4 in which 4-methylproline is replaced by proline and 3,5-difluorophenylalanine is replaced by 3-fluorophenylalanine (FIGS. 4A-4B). In analogy to the published synthesis of ADEP 4, our plan was to prepare 10a in a convergent fashion. We anticipated that the requisite tripeptide fragment could be synthesized via a Joullié-Ugi 3CR (FIG. 4A). The substrates of the reaction were N-Boc proline, dehydropiperidine, and an isocyanide derived from alanine methyl ester. While N-Boc proline was commercially available, the other two substrates had to be chemically synthesized. The isocyanide was prepared via the N-formylation and dehydration of alanine methyl ester under racemization-free conditions described in the literature (see, e.g., Zhu et al., Tetrahedron Lett. 2008, 50, 577). N-formyl-L-alanine methyl ester was synthesized from L-alanine methyl ester hydrochloride accordingly to literature procedures for the preparation of amino acid tert-butyl esters (see, e.g., Waki et al., J. Org. Chem. 1977, 42, 2019). Dicyclohexylcarbodiimide (DCC) activation of formic acid as the O-acylisourea derivative followed by the addition of the amino acid ester provided the desired N-formyl product 1 in good yield. Dehydration of 1 to form the isocyanide (2) was effected by triphosgene in the presence of N-methylmorpholine (NMM) (Zhu, supra). Synthesis of the isocyanide was realized in 69% yield over two steps. Chiral GC-MS analysis of the isocyanide product revealed that no racemization of the amino acid occurred during the formylation and dehydration.

We envisioned that the cyclic imine substrate of the Joullie-Ugi reaction could be prepared by halogenation and dehydrohalogenation of piperidine (FIG. 4A). N-chlorination of piperidine via in situ generation of tert-BuOCl gave the desired product in quantitative yield (Waki, supra). Dehydrohalogenation of the N-chloropiperidine was effected by sodium methoxide in methanol (Nutt, supra). Due to its instability, the crude dehydropiperidine was directly used in a Joullié-Ugi 3CR with N-Boc-proline and the isocyanide derived from alanine methyl ester (2) (see, e.g., Zhong et al., Tetrahedron Lett. 2005, 46, 1099; Davis et al., Org. Lett. 2002, 4, 103). After stirring for five days at room temperature, the expected tripeptide methyl ester, 3, was isolated in 76% yield. Analytical HPLC analysis of saponified 3 (LiOH, 1:1 THF:H₂O, quantitative yield) revealed that its diastereomeric ratio was 70:30. Based on the retention time of an authentic standard [(S)-Boc-Pro-(S)-Pip-(S)-Ala-COOH], we determined that the desired tripeptide was the minor diastereomer. The basis of the diastereoselectivity of this reaction is not clear and is under investigation. In spite of the undesirable stereoselectivity, the yield and the atom economy of the one-pot Joullié-Ugi 3CR make it a viable alternative to standard peptide chemistry for synthesis of the ADEP 4 tripeptide precursor.

The diastereomeric mixture of tripeptide products were saponified and carried forward to prepare the desired peptidolactone using the convergent synthetic route described in the literature (FIG. 4B) (see, e.g., Hinzen, supra; U.S. 20050107288). In contrast to the reported synthesis of ADEP 4, the diastereomeric peptidolactones were chromatograpically separated and acylated with N-2-heptenoyl, 3-fluorophenylalanine to yield 10a and its diastereomer 10b.

Diversity-Oriented Synthesis of Cyclic Acyldepsipeptides with Conformationally Constrained Amino Acids.

In addition to the efficiency with which an isocyanide-based multicomponent reaction could be used to synthesize a tripeptide, a major consideration in the selection of this reaction type was its applicability in the preparation of structurally diverse peptides. Rather than preparing a random collection of tripeptides, we sought to synthesize tripeptides that were more conformationally constrained than the tripeptide precursor of ADEP 4. Our utilization of conformationally constrained amino acids was an extension of the findings of the Bayer research group wherein replacement of the N-methylalanine moiety of the natural enopeptins with pipecolate yielded the enopeptin derivative ADEP4 with enhanced antibacterial activity (see, e.g., Hinzen, supra; U.S. 20050107288).

Our first synthetic target was an analog of the ADEP 4 tripeptide fragment with a substituent on the pipecolate moiety. Based on the principles of conformational analysis, we predicted that strategic placement of a substituent on the ring would increase the inversion barrier of pipecolate (see, e.g., Eliel, E; Wilen S. H. Stereochemistry of Organic Compounds; John Wiley and Sons: New York, 1994, Chapter 11). In particular, a substituent on the 4-position of pipecolate would be especially rigidifying since ring inversion would result in a strongly disfavored 1,3-diaxial interaction between ring substituents. To prepare such a compound, we carried out a Joullié-Ugi 3CR with N-Boc-proline, the isocyanide derived from alanine methyl ester (2), and dehydro 4-methyl piperidine (FIG. 4A). The latter compound was prepared in an analogous manner to dehydropiperidine. Interestingly, the dehydro-4-methylpiperidine was a better substrate in the Joullié-Ugi 3CR, yielding the expected tripeptide methyl ester in 84% in a reaction time of only 2 days. Analytical HPLC analysis of the saponified product revealed that its diastereomeric ratio was 70:30. As the retention time of the minor diastereomer was very similar to that of the authentic ADEP 4 tripeptide precursor, we deduced that it was the desired diastereomer containing (2S,4R)-4-methylpipecolamide. The mixture of diastereomeric peptides was carried forward in the aforementioned scheme for convergent synthesis of the peptidolactone core structure. The diastereomeric peptidolactones were chromatographically separated and acylated with N-2-heptenoyl, 3-fluorophenylalanine to yield the desired compound, 10c (FIG. 4C).

Our other synthetic targets were tripeptides containing α,α-disubstituted amino acids (FIGS. 5A-5C). These amino acids, while of limited commercial availability, are known to limit the conformation of peptides (see, e.g., Karle et al., Biochemistry. 1990, 29, 6747; Marshall et al., Proc. Natl. Acad. Sci. USA. 1990, 87, 487). We suspected that the desired tripeptides could be prepared from methylamine, N-Boc-proline, the isocyanide derived from L-alanine methyl ester (2), and various ketones in an Ugi 4CR. To avoid mixtures of diastereomeric products, we used symmetric ketones (i.e., 3-pentanone, cyclobutanone, cylopentanone, and cyclohexanone) as substrates (FIG. 5A). The reactants were stirred in MeOH for a period of 1-5 days to optimize reaction conditions. Products 5-8 were isolated in good to excellent yields. The results are summarized in Table 1. Good yields of the tripeptides were only observed with reaction times >4 days and reaction concentrations ≧1.9 M. Increasing the reaction temperature of a model reaction with cyclopentanone and methylamine to 50° C. did not significantly improve the reaction yield. Using four different ketones as substrates in the Ugi 4CR, we were able to prepare four different tripeptide methyl esters (5-8) (FIG. 5A). Those products were saponified as previously described to yield the requisite tripeptides. The tripeptides prepared via the Ugi 4CR were used in the aforementioned convergent synthesis to yield enopeptin derivatives, 10e-h (FIGS. 5B-5C).

TABLE 1 Optimized Ugi 4CR conditions for symmetric ketones Ugi Conc. Temp. Time Yield Product R n (M) (° C.) (d) (%) 5 CH₃ 0 1.90 25 5 75 6 H 1 1.90 25 5 93 7 H 2 0.65 25 5 62 7 H 2 1.90 25 5 78 8 H 3 1.90 25 5 90

The naturally occurring enopeptins and the synthetic derivative ADEP 4 are reported to have strong antibacterial activity (see, e.g., Hinzen et al., Chem Med Chem 2006, 1, 689). Broth dilution assays were used to determine the MICs of the acyldepsipeptide derivatives 10a-h against both ATCC strains and clinical isolates of S. epidermis, S. aureus, and Enterococci obtained from patients of the Veterans Affairs Medical Center in Providence, Rhode Island. Clinical isolates were included to gain a better indication of the potential of these new antibacterial agents (see, e.g., Clinical and Laboratory Standard Institute (CLSI) Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically M07-A8; CLSI 8^(th) ed., Wayne, Pa., 2009; Clinical Laboratory Standards Institute (CLSI) Performance standards for antimicrobial susceptibility testing M100-S19. CLSI 19th informational suppl., Wayne, Pa. 2009). In the interest of assessing the cell-killing ability of these compounds, the minimal bactericidal concentrations (MBC) of the compounds was also determined against the aformentioned strains. The MIC was defined as the lowest concentration of an antimicrobial agent visually inhibiting more than 99% of the colonies. The MBC was defined as the lowest antibiotic concentration to show no growth (99.9% kill) after 24 h of incubation.

Compound 10a, an analog of ADEP 4, exhibited the expected antibacterial activity against drug-resistant, pathogenic S. aureus strains. All synthetic acyldepsipeptides in which the pipecolate moiety was replaced by α,α-disubstituted amino acids lacked antibacterial activity. In contrast, compound 10c, which 4-methylpipecolate in place of pipecolate, had better activity than compound 10a against MSSA. Compound 10a was also evaluated against Staphylococcus epidermis (ATCC 25984) and showed an MIC of 1.25 μg/mL and an MBC of 1.25 μg/mL.

TABLE 2 Biological activity of synthetic acyldepsipeptides vs. S. aureus (μg/mL) MSSA MRSA MIC MBC MIC MBC 10a 1.25 1.25 1.25 1.25 10b >312 >312 >312 >312 10c 0.6 0.6 0.6 2.4 10d >156 >156 >156 .156 10e 78.1 >312 >312 >312 10f 312 >312 >312 >312 10g 39.1 >312 >312 >312 10h 39.1 >312 >312 >312 MSSA = Methicillin-susceptible S. aureus (ATCC 35556) MRSA = Methicillin-resistant S. aureus (clinical isolate from blood)

Based on the activities of compounds 10a and 10c against the S. aureus strains, they were selected for further evaluation against a panel of pathogenic Enterococci. Remarkably, compound 10c exhibited more potent activity against E. faecalis and vancomycin-resistant E. faecium than compound 10a.

TABLE 3 Biological activity of synthetic acyldepsipeptides vs. Enterococci (μg/mL) EF¹ EF² VRE³ VRE⁴ MIC MBC MIC MBC MIC MBC MIC MBC 10a 0.16 1.25 0.04 0.04 0.08 0.08 0.04 0.04 10c 0.04 0.08 0.02 0.04 0.04 0.08 0.04 0.04 ¹= Enterococcus faecalis (ATCC 29212) ²= Enterococcus faecalis (clinical isolate from rectal swab) ³= Vancomycin-resistant Enterococcus faecium (clinical isolate obtained from tissue) ⁴= Vancomycin-resistant Enterococcus faecalis (clinical isolate from rectal swab)

Experimental

All amino acids and peptide coupling reagents were purchased from NovaBiochem. Additional chemicals were purchased from Sigma-Aldrich unless otherwise stated. A Biotage Initiator microwave reactor was used. GC-MS analysis was performed on a Hewlett Packard 5971A GC-MS system using an HP5-MS column and helium as the carrier gas. Splitless injections of 1 mL were made using an initial temperature of 60° C., holding 2 min, then 20° C./min ramp to 280° C., and holding 2 min. Chiral GC-MS was performed on a Hewlett Packard G1800C instrument equipped with a Varian CP-Chirasil-DEX 25 m×0.32 mm column. Low-resolution analytical LC-MS was performed in the positive ion mode on a Thermo LCQ Deca XP MAX high sensitivity MS^(n) ion trap mass spectrometer with a Shimadzu HPLC system using a Waters X-Terra MS C₁₈ column (2.5 μm, 2.1×50 mm). The method consisted of 5-95% MeCN in H₂0+0.1% TFA over 15 min. The flow rate was 0.2 mL/min. High-resolution mass analyses were performed on a JOEL JMS-600H double focusing magnetic sector mass spectrometer using FAB ionization. NMR analyses were performed on a Bruker Avance Ultrashield spectrometer (400 MHz for ¹H, 100 MHz for ¹³C). All spectra were referenced to residual solvent signals in CDCl₃ (7.24 ppm for ¹H, 77.0 ppm for ¹³C.)

Preparation of Substrates for Multicomponent Reactions.

N-formyl-L-alanine methyl ester (1):

Dicyclohecylcarbodiimide (DCC) (10 g, 48.5 mmol) was dissolved in 50 mL of DCM and cooled to 0° C. for 5 min. 96% formic acid (2.6 mL, 69 mmol) was added slowly. In a separate flask, L-alanine methyl ester HCl salt (5 g, 36 mmol) was dissolved in 25 mL dichloromethane (DCM) with 7 mL NMM+1 g of DMAP. The contents of this flask were added to the DCC-formic acid mixture at 0° C. and the reaction allowed to warm to room temperature overnight with stirring. The majority of the solvent was removed in vacuo until a viscous slurry was obtained. This slurry was vacuum filtered through silica gel and the residue was washed with 25 mL DCM to ensure complete elution of product. The filtrate was concentrated in vacuo and loaded on a 75×50 mm Si gel resin bed and eluted with 4:1 EtOAc:hexanes. Yield: 3.4 g (72.1%), clear oil, R_(f)=0.6 (4:1 EtOAc:hexanes), stains white with p-anisaldehyde. ¹H NMR (CDCl₃) 8.14 (1H, s), 6.43 (1H, bs), 4.54 (1H, m), 3.72 (3H, s), 1.39 (3H, d, J=7 Hz). ¹³C NMR (CDCl₃) 173.0, 160.5, 52.6, 46.7, 18.4. MS (EI, m/z): 131.0 [M]⁺ for C₄H₉NO₂.

Isocyanide derived from alanine methyl ester (2):

N-formyl-L-alanine methyl ester (1) (2.2 g, 16.8 mmol) was dissolved in 50 mL anhydrous DCM and solution cooled to −78° C. In a separate, dry, pear shaped flask was added triphosgene (1.7 g, 5.7 mmol) and 7 mL dry DCM. If the triphosgene begins to bubble during the addition of DCM discard it carefully, as it has become wet. The triphosgene solution was added slowly to the N-formyl amino acid ester. Then 3.6 mL (33 mmol) N-methylmorpholine (NMM) added slowly over 10 min. The reaction was stirred for 1.5 h at −78° C. then quenched with 22 mL deionized water by placing a vent needle in the septa and allowing the stirring solution to warm to room temperature. The resulting mixture was partitioned and the water layer washed with an additional 50 mL DCM. The organic fraction was collected, dried over Na₂SO₄, and solvent removed in vacuo. Crude product was loaded on a 75×50 mm Si gel resin bed and eluted with 4:1 hexanes:EtOAc (R_(f)=0.65, Iodine/Si stain). Pale yellow oil, Yield: 1.8 g (95%). ¹H NMR (CDCl₃) 4.32 (1H, q), 3.81 (3H, s), 1.63 (3H, d, J=8 Hz). ¹³C NMR (CDCl₃) 167.3, 159.0, 60.0, 51.3, 19.3. MS (EI, m/z): 113.0 [M]⁺ for C₅H₇NO₂.

N-chloropiperidine: 5.8 mmol (0.55 mL) of tert-BuOH, 11.7 mmol (1.39 mL) piperidine were added to 30 mL MTBE and stirred at 0° C. 11.8 mmol (23.5 mL) cleaning bleach and 11.8 mmol (0.68 mL) of acetic acid were added together slowly and reaction mixture was stirred at 0° C. for 30 min. Reaction mixture was then quenched with 15 mL of water, extracted with 20 mL MTBE, and the organic layer was washed with brine and dried with Na₂SO₄. Evaporation of solvent under reduced pressure gave the desired product 1.4 g (10.5 mmol, 89% yield) as a pale yellow oil. R_(f)=0.9 (3:1 EtOAc:hexanes) MS (EI, m/z): 119.1 [M]⁺ for C₅H₁₀NCl.

Dehydropiperidine: 10.5 mmol (1.4 g) of N-chloropiperidine was dissolved in 3.5 mL (5.71 mmol) of 25% by wt NaOMe in MeOH. The reaction was stirred for 10 min. under N₂, after which a white precipitate of NaCl was formed and the reaction was complete.

Synthesis of N-2-heptenoyl-3-fluorophenylalanine-COOH (9):

N-Boc-L-3-fluorophenyl-L-alanine (500 mg, 1.76 mmol) and NaHCO₃ (300 mg, 3.6 mmol) were dissolved in 10 mL DMF. MeI (1 mL, 16 mmol) was added dropwise and the mixture stirred for 24 h. Reaction mixture was then partition in 25 mL EtOAc 25 mL 0.1N HCl and 25 mL brine, then dried over Na₂SO₄ and concentrated in vacuo. Yield: 500 mg (1.68 mmol, 96%). N-Boc-L-3-fluorophenyl-L-alanine methyl ester product (500 mg, 1.7 mmol) was dissolved in 6.75 mL DCM and 4.3 mL 9:1 TFA:H₂O added at 0° C. Reaction was allowed to warm up to room temperature and stirred for 2 h 2×100 mL toluene successively added and removed in vacuo. Yield: 510 mg of TFA salt of L-3-fluorophenyl-L-alanine methyl ester (1.63 mmol, 93%). The product (650 mg, 2.09 mmol) was dissolved in 25 mL dry DCM and 3 mL DIEA added and was added to a separate flask containing HATU (1.14 g, 3 mmol) and trans-2-heptenoic acid (350 μL, 2.6 mmol) in 15 mL DCM and the mixture stirred overnight. The reaction mixture was then washed with 30 mL 0.1N HCl, dried over Na₂SO₄ and concentrated under vacuum, then purified by flash Si gel chromatography with 1:1 EtOAc:hexanes as eluent. R_(f)=0.95 (1:1 EtOAc:hexanes). N-2-heptenoyl-3-fluorophenylalanine methyl ester (400 mg, 1.3 mmol) was dissolved in 4 mL 1:1 THF:H₂O, then LiOH.H₂O (149 mg, 3.55 mmol) added and reaction stirred for 30 min. 1N HCl was added to adjust the pH to 1, THF removed under vacuum and the resulting aqueous layer extracted with 2×20 mL EtOAc, which was then dried with Na₂SO₄ and concentrated under vacuum. Yield: 400 mg (100%) of 9. ¹H NMR (CDCl₃) 7.18 (1H, m), 6.88 (4H, m), 6.37 (1H, d, J=8 Hz), 5.77 (1H, d, J=16 Hz), 4.91 (1H, d, J=8 Hz), 3.22 (1H, m) 3.12, (1H, m), 2.13 (2H, m), 1.33 (4H, m), 0.86, (3H, m). ¹³C NMR (CDCl₃, mixture of rotamers) 174.2, 167.0, 164.1, 161.7, 147.5, 138.5, 130.3, 125.4, 122.7, 116.6, 114.4, 53.7, 37.1, 32.0, 30.2, 22.3, 13.9. HRMS (FAB): calcd for C₁₆H₂₀NO₃FNa [M+Na]⁺ 316.1325, obsd 316.1306 (Δ=6.0 ppm).

Procedure for the Joullié-Ugi 3CR

The crude cyclic imines, 4 mL dry MeOH and N-Boc-L-proline (1.95 g, 8.5 mmol) were added directly to the reaction mixture, and were stirred for 15 min. The isocyanide 2 (780 mg, 6.9 mmol) was added, and the reaction stirred for 2-5 days. Solvent was removed under vacuum and crude mixture was purified on a Si gel column with 7:3 EtOAc:hexanes eluent.

Diastereomeric ratio determinations of the saponified Joullié-Ugi 3CR products were determined using a Haisil-100 C18 column (5 micron, 150 mm×4.6 mm). The flow rate was 1.5 mL/min. The method consisted of 20-65% MeCN in H₂0+0.1% TFA over 20 min. The detector was set to 214 nm. The retention times of the diastereomeric products were 7.63 and 8.58 min. The retention time of authentic N-Boc-L-Pro-L-Pip-L-Ala-COOH prepared according to the literature was 7.65 min (US 2005/0107288).

N-Boc-Pro-pipecolate-Ala-OMe (3):

Yield: 2.16 g (5.2 mmol, 76%). R_(f)=0.3 (7:3 EtOAc:hexanes) ¹H NMR (CDCl₃, mixture of diasteromers) 8.45 (d, 0.5H), 7.38, (d, 0.5H), 4.52 (m, 1H), 4.48 (m, 1H), 4.42 (m, 1H), 3.85 (d, 0.5H), 3.67 (s, 3H), 3.44 (1H, m), 3.40 (1H, m), 2.45 (1H, m), 2.08 (2H, m), 1.87 (3H, m), 1.64 (2H, m) 1.35 (12H, s), 0.99 (m, 2H). ¹³C NMR (CDCl₃): 173.3, 172.1, 170.0, 154.4, 79.6, 55.4, 52.0, 49.9, 48.1, 46.7, 43.4, 39.4, 34.4, 29.3, 28.0 (3C), 25.7, 24.5, 20.3, 16.6. HRMS (FAB): calcd for C₂₀H₃₃N₃O₆Na [M+Na]⁺ 434.2267, obsd 434.2267 (Δ=5.8 ppm).

N-Boc-Pro-4-methylpipecolate-Ala-OMe (4):

Yield: 2.47 g (5.8 mmol, 84%). R_(f)=0.3 (7:3 EtOAc:hexanes) ¹H NMR (CDCl₃, mixture of diasteromers): 8.39 (d, 0.5H), 7.28, (d, 0.5H), 4.55 (m, 1H), 4.48 (m, 1H), 4.40 (m, 1H), 3.85 (d, 0.5H), 3.65 (s, 3H), 3.49 (1H, m), 3.41 (1H, m), 2.43 (1H, m), 2.05 (2H, m), 1.83 (3H, m), 1.64 (2H, m) 1.38 (12H, s), 0.99 (m, 2H), 0.85 (3H, d). ¹³C NMR (CDCl₃): 173.4, 172.1, 170.1, 154.6, 79.8, 56.4, 52.2, 48.5, 47.0, 43.4, 34.4, 33.1, 29.5, 29.4, 28.4 (3C), 27.1, 24.9, 21.8, 16.9. HRMS (FAB): calcd for C₂₁H₃₅N₃O₆Na [M+Na]⁺ 448.2424, obsd 448.2406 (Δ=4.1 ppm).

Procedure for the Ugi 4CR

Ketones (9.48 mmol) was added to a solution of 40% methylamine in MeOH (4.75 mL, 9.48 mmol) and allowed to precondense for 1.5 h. N-Boc-L-proline (2.04 g, 9.48 mmol) added and resulting mixture stirred for 15 min., then isocyanide derived from L-alanine methyl ester (1.08 g, 9.48 mmol) was added. Reaction was left to stir for 5 days at room temperature, then concentrated in vacuo. Crude product was loaded onto a 80 mm×50 mm Si gel resin bed and eluted with 7:3 EtOAc:hexanes.

3-Pentanone Ugi Tripeptide (5):

Yield 3.03 g (7.11 mmol, 75%). R_(f)=0.25 (7:3 EtOAc:hexanes), stains white with p-anisaldehyde. ¹H NMR (CDCl₃, mixture of rotamers) 6.35 (1H, d), 4.59 (1H, m), 3.70 (3H, s), 3.50 (1H, m), 3.45 (1H, m), 3.08 (3H, s), 2.23 (2H, m), 2.10 (2H, m), 1.85 (4H, m), 1.48 (3H, d), 1.38 (9H, s), 0.87 (3H, m) 0.78 (3H, m). ¹³C NMR (CDCl₃, mixture of rotamers) 173.9, 173.6, 172.9, 157.1, 154.7, 79.6, 68.7, 68.2, 58.0, 57.7, 52.0, 50.5, 48.5, 46.9, 32.5, 29.2, 28.5 (3C), 26.1, 24.2, 24.0, 17.7. HRMS (FAB): calcd for C₂₁H₃₇N₃O₆Na [M+Na]⁺ 450.2580, obsd 450.2566 (Δ=3.1 ppm).

Cyclobutanone Ugi Tripeptide (6):

Yield: 3.62 g (8.81 mmol, 93%). R_(f)=0.25 (7:3 EtOAc:hexanes), stains white with p-anisaldehyde. ¹H NMR (CDCl₃, mixture of rotamers) 7.65 (1H, d), 4.42 (2H, m), 3.52 (3H, s), 3.45 (1H, m), 3.40 (1H, m), 2.87 (3H, s), 2.54 (4H, m), 2.03 (3H, m), 1.65 (2H, m), 1.54 (1H, m), 1.38 (3H, d), 1.28 (9H, s). ¹³C NMR (CDCl₃, mixture of rotamers) 173.7, 173.3, 173.2, 154.7, 153.6, 79.7, 65.6, 60.5, 56.7, 53.6.0, 52.2, 48.1, 46.9, 33.2, 31.8, 28.5 (3C), 24.5, 23.4, 17.5, 14.5. HRMS (FAB): calcd for C₂₀H₃₃N₃O₆Na [M+Na]⁺ 434.2267, obsd 434.2282 (Δ=3.4 ppm).

Cyclopentanone Ugi Tripeptide (7):

Yield: 3.12 g (7.33 mmol, 78%). R_(f)=0.25 (7:3 EtOAc:hexanes), stains white with p-anisaldehyde. ¹H NMR (CDCl₃, mixture of rotamers) 7.65 (1H, d), 4.54 (1H, m), 4.40 (1H, m), 3.65 (3H, s), 3.60 (1H, m), 3.45 (1H, m), 3.00 (3H, s), 2.52 (1H, m), (2.11-1.52 (12H, m) 1.43 (9H, s), 1.38 (3H, d). ¹³C NMR (CDCl₃, mixture of rotamers) 175.4, 173.6, 171.0, 154.4, 153.5, 79.4, 73.4, 73.0, 60.2, 58.0, 57.9, 52.0, 50.5, 48.2, 46.9, 36.2, 35.5, 34.8, 33.0, 29.2, 28.3 (3C), 24.2, 24.0, 23.1, 22.4, 17.6, 14.1. HRMS (FAB): calcd for C₂₁H₃₅N₃O₆Na [M+Na]⁺ 448.2424, obsd 448.2432 (Δ=1.8 ppm).

Cyclohexanone Ugi Tripeptide (8):

Yield: 3.75 g (8.53 mmol, 90%). R_(f)=0.25 (7:3 EtOAc:hexanes), stains white with p-anisaldehyde. ¹H NMR (CDCl₃, mixture of rotamers) 6.72 (1H, m), 4.51 (1H, m), 4.37 (1H, m) 3.54 (3H, s), 3.45 (1H, m), 3.35 (1H, m), 2.98 (3H, s), (2.11-1.52 (14H, m) 1.43 (9H, s), 1.38 (3H, d). ¹³C NMR (CDCl₃, mixture of rotamers) 175.6, 173.7, 171.1, 154.5, 79.4, 66.6, 65.8, 60.2, 58.6, 52.2, 48.1, 46.7, 32.9, 32.4, 31.8, 30.4, 29.5, 28.5 (3C), 24.2, 22.8, 21.9, 20.9, 18.1, 17.7, 14.1. HRMS (FAB): calcd for C₂₂H₃₇N₃O₆Na [M+Na]⁺ 462.2580, obsd 462.2562 (Δ=3.9 ppm).

Procedure for the saponification of tripeptides: The tripeptide methyl esters (1.55 g, 3.62 mmol) were dissolved in 10.4 mL 1:1 THF:H₂O solution and LiOH.H₂O (356 mg, 8.47 mmol) added. Reaction was stirred for 2.5 h then quenched with 10 mL 1N HCl. THF was removed under vacuum and aqueous layer was extracted with 2×20 mL EtOAc. Organic layer was dried over Na₂SO₄ and concentrated under vacuum.

Procedure for Synthesis of Acyldepsipeptides (10a-h)

Linear Pentapeptolide Formation and Deprotection: Tripeptides (3.9 mmol), TPTU (1.45 g, 4.88 mmol), HOBt (770 mg, 5.7 mmol) and DIEA (2 mL, 11.5 mmol) were dissolved in 20 mL dry DCM and allowed to stir under N₂, at RT for 10 min. Depsipeptide (NH₂-Pro-N-CBz-Ser-phenacylester) (2.2 g, 3.9 mmol) was dissolved in 10 mL dry DCM and added dropwise over 5 min (see, e.g., US 20050107288). After 15 h the reaction mixture was concentrated in vacuo and then redissolved in 50 mL EtOAc. The EtOAc solution was extracted sequentially with 20 mL each of 0.2N HCl, saturated NaHCO₃ and brine. The organic layer was dried over Na₂SO₄ and concentrated in vacuo. The product was purified over a 110×55 mm bed of silica gel using 20:0.5 EtOAc:MeOH. Blue spots with R_(f) 0.3 were visualized with ceric ammonium molybdenate.

Pentapeptolides (1.3 mmol) were phenacyl deprotected by dissolving in 1.45 mL 90% AcOH in H₂O, then Zn dust (580 mg, 9.07 mmol) added and reaction stirred for 30 min. Zn was filtered through cotton and residue washed with 10 mL EtOAc and 10 mL 1N HCl. 30 mL EtOAc was added to the filtrate and it was washed with 3×20 mL 1N HCl. Organic layer was dried with Na₂SO₄ and concentrated under vacuum. Yield: 945 mg (100%). R_(f)=0.2 (20:1 EtOAc:MeOH).

Macrocyclization: Pentafluorophenol esters were prepared from phenacyl deprotected linear peptides (1.37 mmol), by dissolving in 5.25 mL dry DCM and adding pentafluorophenol (1 g, 5.43 mmol) and EDC (285 mg, 1.64 mmol) at −78° C. Reaction was allowed to warm to room temperature overnight with stirring, then concentrated under vacuum. Crude pentafluorophenol esters (approximately 2 g) were Boc deprotected by treatment with 8.35 mL 3N HCl in EtOAc at 0° C. and stirred at 0° C. for 3.5 h. For cyclization the crude reaction mixture is diluted into 417 mL DCM and added dropwise at a rate of ˜1 drop/sec to a vigorously stirring solution of 324 mL sat. NaHCO₃ and 557 mL DCM. Reaction was left to stir overnight. Organic layer was collected and dried over Na₂SO₄ and concentrated in vacuo, then purified over a 100×25 mm Si gel column with 20:1 EtOAc:MeOH eluent. In the case of diastereomers derived from 3 and 4, the compound with an R_(f)=0.3 has (2S)-pipecolate and the compound with an R_(f)=0.2 has (2R)-pipecolate.

Spectral data for S-Pip-CBz-macrocycle derived from 3:

¹H NMR (CDCl₃) 8.30 (1H,d, J=8 Hz), 7.28 (4H, m), 5.68 (1H, d, J=8 Hz), 5.15 (1H, m), 5.03 (2H, m), 4.99 (1H, m), 4.74 (1H, d, J=8 Hz), 4.66 (1H, s), 4.49 (2H, m), 4.17 (1H, t), 4.06 (1H, dd), 3.72 (2H, m), 3.65 (1H, m), 3.50 (2H, m), 2.68 (1H, d, J=12 Hz), 2.52 (1H, m), 2.31 (1H, m), 2.11 (3H, m), 1.91 (7H, m), 1.68 (1H, m), 1.58 (1H, m), 1.36 (5H, m). ¹³C NMR (CDCl₃) 173.3, 171.5, 169.6, 168.5, 166.2, 156.2, 135.9, 128.5, 128.3 (3H), 128.0, 67.9, 65.8, 60.3, 58.9, 57.1, 56.6, 53.9, 53.4, 48.0, 46.8, 46.3, 41.0, 30.9, 30.6, 28.2, 24.8, 23.1, 21.3, 18.0, 14.1. HRMS (FAB): calcd for C₃₀H₃₉N₅O₈Na [M+Na]⁺ 620.2696, obsd 620.2681 (Δ=2.4 ppm).

Spectral data for S-4-Me-Pip-CBz-macrocycle derived from 4:

¹H NMR (CDCl₃) 8.31 (1H,d, J=8 Hz), 7.28 (4H, m), 5.63 (1H, d, J=8 Hz), 5.17 (1H, m), 5.03 (2H, m), 4.99 (1H, m), 4.76 (1H, d, J=8 Hz), 4.67 (1H, s), 4.50 (2H, m), 4.19 (1H, t), 4.08 (1H, dd), 3.72 (2H, m), 3.66 (1H, m), 3.49 (2H, m), 2.68 (1H, d, J=12 Hz), 2.53 (1H, m), 2.31 (1H, m), 2.12 (3H, m), 1.94 (7H, m), 1.56 (2H, m), 1.36 (3H, m), 1.02 (2H, m), 0.96 (3H, m). ¹³C NMR (CDCl₃) 173.2, 171.5, 169.7, 168.6, 166.2, 156.2, 135.8, 128.4, 128.3 (3H), 128.0, 67.9, 65.8, 60.3, 58.8, 57.1, 56.7, 53.9, 48.0, 46.9, 46.3, 40.7, 36.3, 33.1, 30.8, 30.5, 27.9, 23.0, 21.7, 21.2, 17.9. HRMS (FAB): calcd for C₃₀H₃₉N₅O₈Na [M+Na]⁺ 634.2853, obsd 634.2868 (Δ=2.4 ppm).

Deprotection of Macrocycles: Cbz-protected macrocycles (0.16 mmol) were deprotected using 75 mg 10% Pd/C and 100 mg NH₄COOH were dissolved in 4 mL isopropanol heated in a microwave reactor for 8 min at 85° C. (Daga et al., Tetrahedron Lett. 2001, 42, 5191). The reaction mixture was then filtered through celite, the residue washed with MeOH and the filtrate concentrated under vacuum. The CBz deprotected macrocycles (0.1 mmol) were coupled to 9 (44 mg, 0.15 mmol) in 800 μL DMF containing TPTU (50 mg, 0.17 mmol), HOBt (20 mg, 0.15 mmol), and 60 μL diisopropylethyamine. The reaction was stirred overnight at room temperature.

Purification of acyldepsipeptides (10a-h) compounds was accomplished using a Phenomenex Gemini C18 (10 micron, 150×10 mm, 110 Å). The method consisted of 20-80% MeCN in H₂0+0.1% TFA over 20 min. The detector was set to 214 nm. The flow rate was 10 mL/min.

Acyldpesipeptide 10a:

Isolated yield from deprotected peptidolactone: 25 mg (0.034 mmol, 34%) white amorphous powder. ¹H NMR (CDCl₃) 8.55 (1H, d, J=8 Hz), 7.26 (0.5H, m), 7.22 (0.5H, m), 6.99 (1H, m), 6.89 (3H, m), 6.52 (1H, d, J=12 Hz), 6.17 (1H, d, J=16 Hz), 5.12 (1H, m), 4.98 (1H, m), 4.75 (1H, d, J=12 Hz), 4.67 (2H, m), 4.55 (1H, m), 4.48 (2H, m), 3.73 (1H, m), 3.61 (1H, m), 3.51 (2H, m), 3.30 (1H, m), 2.94 (2H, m), 2.71 (1H, m), 2.62 (1H, m), 2.34 (1H, m), 2.38 (4H, m), 1.92 (6H, m), 1.75 (1H, m), 1.64 (1H, m), 1.40 (1H, m), 1.38 (3H, m), 1.32 (4H, m), 0.88 (3H, m). ¹³C NMR (CDCl₃) 172.5, 171.2, 170.9, 169.4, 166.4, 165.0, 164.0, 161.5, 146.2, 138.6, 130.0, 125.2, 123.1, 116.5, 116.4, 113.8, 113.6, 65.0, 59.0, 57.1, 56.8, 54.7, 51.2, 47.8, 47.0, 46.4, 41.3, 38.4, 31.8, 30.7, 30.4, 28.0, 24.9, 23.1, 22.2, 21.3, 18.0, 13.8. HRMS (FAB): calcd for C₃₈H₅₁N₆O₈FNa [M+Na]⁺ 761.3650, obsd 761.3625 (Δ=3.3 ppm).

Acyldpesipeptide 10b:

Isolated yield from deprotected peptidolactone: 26 mg (0.035 mmol, 35%) white amorphous powder. ¹H NMR (CDCl₃, mixture of rotamers) 8.03 (1H, m), 7.45 (1H, m), 7.18 (1H, m), 6.99 (4H, m), 6.85 (1H, m), 6.75 (1H, m), 6.56 (0.6H, m), 5.90 (1H, d), 5.80 (1H, d), 5.38 (1H, d), 5.30 (2H, m), 4.92 (3H, m), 4.76 (2H, m), 4.37 (1H, m), 4.33 (1H, m), 3.97 (1H, m), 3.80 (1H, m), 3.75 (2H, m), 3.63 (3H, m), 3.25 (3H, m), 3.10 (1H, m), 2.92 (1H, m), 2.65 (1H, m), 2.10 (4H, m), 2.01 (10H, m), 1.52 (2H, m), 1.45 (4H, m), 1.38 (3H, m), 0.85 (3H, m). ¹³C NMR (CDCl₃, mixture of rotamers) 172.2, 170.9, 170.3, 167.7, 167.3, 166.0, 163.8, 161.1, 129.7, 129.6, 125.0, 123.3, 116.3, 113.3, 61.2, 60.0, 56.1, 53.1, 48.5, 47.5, 47.2, 46.3, 44.7, 31.7, 30.1, 28.8, 28.7, 26.2, 25.6, 25.5, 25.0, 22.1, 20.6, 17.3, 13.4. HRMS (FAB): calcd for C₃₈H₅₁N₆O₈FNa [M+Na]⁺ 761.3650, obsd 761.3638 (Δ=1.6 ppm).

Acyldpesipeptide 10c:

Isolated yield from deprotected peptidolactone: 23.4 mg (0.034 mmol, 31%) white amorphous powder. ¹H NMR (CDCl₃) 8.89 (1H, bs), 8.51 (1H, d, J=12 Hz), 8.42 (0.5H, bs) 7.93 (0.5H, bs), 7.16 (1H, m), 6.88 (4H, m), 6.20 (1H, d, J=16 Hz), 5.14 (1H, m), 4.98 (1H, m), 4.73 (3H, m), 4.67 (1H, m), 4.50 (2H, m), 3.75 (1H, m), 3.55 (3H, m), 3.30 (1H, m), 2.94 (2H, m), 2.70 (2H, m), 2.31 (1H, m), 2.14 (3H, m), 1.88 (5H, m), 1.62 (2H, m), 1.38 (3H, m), 1.30 (5H, m), 0.94 (3H, m), 0.86 (3H, m). ¹³C NMR (CDCl₃) 172.5, 171.1, 170.8, 169.6, 167.1, 165.1, 164.0, 161.6, 147.0, 138.4, 130.2, 125.2, 122.9, 116.5, 114.0, 65.0, 59.1, 57.1, 57.2, 57.0, 55.2, 51.1, 47.9, 47.1, 46.6, 41.0, 38.4, 36.2, 33.3, 31.9, 30.8, 30.4 (2C), 28.0, 23.1, 22.2, 21.9, 18.0, 13.8. HRMS (FAB): calcd for C₃₉H₅₃N₆O₈FNa [M+Na]⁺ 775.3807, obsd 775.3820 (Δ=1.7 ppm).

Acyldpesipeptide 10d:

Isolated yield from deprotected peptidolactone: 22.1 mg (0.03 mmol, 30%) white amorphous powder. ¹H NMR (CDCl₃, mixture of rotamers) 8.02 (1H, m), 7.74 (1H, bs), 7.51 (2H, m), 7.16 (1H, m), 6.96 (4H, m), 6.74 (1H, m), 5.96 (1H, m), 5.35 (0.5H, m), 5.30 (1H, m), 5.20 (0.5H, m), 4.82 (3H, m), 4.75 (1H, m), 4.40 (1H, m), 4.22 (1H, m), 4.01 (1H, m), 3.56 (3H, m), 3.25 (2H, m), 2.94 (1H, m), 2.62 (1H, m), 2.25 (3H, m), 2.02 (6H, m), 1.86 (5H, m), 1.62 (1H, m), 1.38 (3H, m), 1.30 (4H, m), 0.93 (3H, m), 0.85 (3H, m). ¹³C NMR (CDCl₃, mixture of rotamers) 172.1, 171.8, 171.3, 170.5, 170.2, 168.8, 161.5, 145.4, 140.2, 129.7, 124.8, 123.4, 116.4, 116.1, 113.4, 61.0, 60.3, 57.6, 56.6, 54.2, 53.3, 50.9, 47.5, 47.2, 46.4, 44.4, 40.9, 38.0, 33.9, 33.2, 32.8, 31.9, 30.4, 29.7, 28.9, 28.2, 27.3, 26.2, 25.7, 22.2, 21.7, 18.1, 15.1, 13.9. MS (ESI, m/z): 775.8 [M+Na]⁺ for C₃₉H₅₃N₆O₈F. Acyldpesipeptide 10e:

Isolated yield from deprotected peptidolactone: 22.0 mg (0.037 mmol, 37%) white amorphous powder. ¹H NMR (CDCl₃, mixture of rotamers) 7.69 (1H, d), 6.99 (1H, d), 7.18 (1H, m), 6.94 (4H, m), 6.75 (1H, m), 5.94 (1H, d), 5.75 (1H, m), 5.58 (1H, m), 5.02 (1H, m), 4.90 (1H, m), 4.80 (2H, m), 4.62 (2H, m), 4.00 (1H, m), 3.70 (3H, m), 3.60 (2H, m), 3.28 (2H, m), 2.92 (1H, m), 2.60 (1H, m), 2.27 (3H, m), 2.02 (6H, m), 1.86 (5H, m), 1.72 (1H, m), 1.38 (3H, m), 1.30 (4H, m), 0.93 (3H, m), 0.85 (3H, m). MS (ESI, m/z): 777.4 [M+Na]⁺ for C₃₉H₅₃N₆O₈F.

Acyldpesipeptide 10f:

Isolated yield from deprotected peptidolactone: 25 mg (0.034 mmol, 34%) white amorphous powder. ¹H NMR (CDCl₃, mixture of rotamers) 7.52 (1H, d), 7.47 (1H, d), 7.15 (1H, m), 6.82 (4H, m), 5.90 (1H, d, J=16 Hz), 5.30 (1H, d), 4.92 (2H, m), 4.54 (1H, m), 4.40 (1H, m), 4.23, 1H, m), 3.85 (1H, d, J =12 Hz), 3.58 (3H, m), 3.34 (1H, m), 2.91 (3H, s), 2.85 (1H, m), 2.62 (2H, m), 2.06 (4H, m), 1.98 (4H, m), 1.81 (2H, d), 1.23 (4H, m), 0.85 (3H, m). ¹³C NMR (CDCl₃, mixture of rotamers) 172.4, 172.2, 171.0, 166.6, 161.6, 145.5, 140.2, 129.9, 125.3, 123.3, 116.5, 113.6, 66.8, 61.1, 60.2, 58.0, 56.9, 54.3, 51.2, 47.5, 38.0, 34.2, 32.9, 31.9, 30.3, 29.7, 29.4, 28.6, 28.1, 26.4, 26.2, 25.7, 23.3, 22.7, 22.2, 15.6, 15.3, 14.1, 13.9. MS (ESI, m/z): 761.3 [M+Na]⁺ for C₃₈H₅₁N₆O₈F.

Acyldpesipeptide 10g:

Isolated yield from deprotected peptidolactone: 23 mg (0.030 mmol, 30%) white amorphous powder. ¹H NMR (CDCl₃, mixture of rotamers) 7.70 (1H, m), 7.49 (1H, m), 7.20 (1H, m), 6.97 (2H, m), 6.88 (1H, m), 6.72 (1H, m), 5.92 (1H, d, J=16 Hz), 5.35 (1H, d, J=12 Hz), 4.90 (2H, m), 4.83 (1H, m), 4.61 (1H, d), 4.37 (1H, m), 3.86 (1H, d, J=12 Hz), 3.69 (2H, m), 3.58 (1H, m), 3.49 (1H, m), 3.40 (1H, m), 3.19 (3H, s), 2.91 (1H, m), 2.60 (1H, m), 2.21 (2H, m), 2.10 (2H, m), 2.00 (2H, m), 1.92 (2H, m), 1.33 (3H, m), 0.85 (3H, m). ¹³C NMR (CDCl₃, mixture of rotamers) 174.0, 173.2, 172.6, 171.8, 171.2, 170.2, 167.3, 166.7, 163.9, 161.5, 155.6, 140.5, 129.6, 125.1, 116.4, 113.2, 79.5, 74.6, 61.0, 60.8, 60.0, 59.4, 59.0, 56.2, 51.1, 47.5, 46.1, 38.5, 37.9, 36.9, 35.5, 35.1, 33.4, 31.9, 29.4, 28.2, 27.9, 26.4, 25.8, 25.0, 24.6, 23.5, 22.6, 18.2, 15.6, 14.1. MS (ESI, m/z): 775.6 [M+Na]⁺ for C₃₉H₅₅N₆O₈FNa.

Acyldpesipeptide 10h:

Isolated yield from deprotected peptidolactone: 24 mg (0.032 mmol, 32%) white amorphous powder. ¹H NMR (CDCl₃, mixture of rotamers) 7.76 (1H, d, J=8 Hz), 7.48 (1H, d, J=4 Hz), 7.20 (1H, m), 6.82 (4H, m), 5.90 (1H, d, J=16 Hz), 5.36 (1H, d, J=8 Hz), 4.92 (2H, m), 4.72 (1H, m), 4.37 (1H, m), 3.70 (1H, m), 3.58 (2H, m), 3.39 (2H, m), 3.18 (3H, s), 2.24 (2H, m), 2.05 (6H, m), 1.83 (1H, m), 1.63 (1H, m), 1.38 (3H, m), 0.85 (3H, m). ¹³C NMR (CDCl₃, mixture of rotamers) 174.7, 171.4, 170.7, 170.3, 167.2, 166.4, 145.9, 140.3, 129.7, 124.9, 123.3 (2C), 116.3, 113.4, 69.9, 61.1, 60.2, 60.0, 59.2, 54.4, 51.0, 47.4, 46.4, 40.3, 38.1, 34.5, 33.8, 33.4, 31.9, 29.4, 26.3, 25.7, 23.3, 22.7, 22.2, 18.5, 18.1, 14.2, 13.8. MS (ESI, m/z): 789.6 [M+Na]⁺ for C₄₀H₅₅N₆O₈FNa.

Synthesis of allo-threonine Analongs

Synthesis of enopeptide analogs containing allo-threonine instead of serine, i.e., wherein R¹¹ is —CH₃ instead of hydrogen, is further contemplated. Synthesis of such an analog will follow the synthetic method as detailed herein. Allo-threonine may be synthesized following the procedure of Liang et al., Bioorganic and Medicinal Chemistry (2011) 19:852-860. Synthesis of the prolyl-allo-threonine ester fragment may be generated following the procedure of Hinzen et al., Chem Med Chem (2006) 1:689.

Biological Assays

Minimum inhibitory concentrations (MIC) were determined in duplicate using methods outlined by The Clinical and Laboratory Standards Institute. Compounds were dissolved in DMSO and fresh cation-adjusted Mueller-Hinton broth (SMHB; Difco Laboratories, Sparks, Md., USA; 25 μg/mL calcium and 12.5 μg/mL magnesium) was used to dilute antimicrobial agents in a serial 2-fold schedule. Colony counts for the inoculum verification was determined using Tryptic Soy Agar plates (TSA, Difco, Becton Dickinson Co., Sparks, Md., USA). Following incubation, 100 μL of broth was subcultured onto TSA for MBC determination. MIC and MBC determination can be found in Table 2 and 3. Control isolates were obtained from the American Type Culture Collection (ATCC) and were as follows: Methicillin-resistant S. epidermidis (MRSE ATCC 35984); MSSA (ATCC 35556) and, VRE (ATCC 2030).

Example 2 Enopeptins and Virulence

Enopeptins do not suffer from cross-resistance to all antibacterial agents on the market or those in clinical development because their mechanism of action is distinct from all clinically used antibacterial drugs they bind and deregulate the activity of the ClpP protease (see, e.g., Brötz-Oesterhelt et al., Nature Medicine, 10, 1082-1087 (2005); Kirstein et al., EMBO Molecular Medicine. 1, 3-49; Lee et al., Nature Structural Biology (2010) 17:471-479). ClpP (caseinolytic protease) is structurally and functionally analogous to the eukaryotic proteasome (see, e.g., Gottesman, Annual Review of Cell and Developmental Biology. 19, 565-587 (2003); Baker et al., Trends Biochemical Sciences. 31, 647-653 (2006); Singh et al., Proceedings of the National Academy of Science, USA. 97, 8898-8903 (2000); Hsiung et al., FEBS Letters. 581, 3749-3757 (2007); Kessel et al., Journal of Molecular Biology. 250, 587-594 (1995)). As is the case for the proteasome, ClpP monomers self-assemble into two heptameric rings that dimerize to form a large barrel-shaped structure (see, e.g., Hsiung et al., FEBS Letters. 581, 3749-3757 (2007); Wang et al., Cell. 91, 447-456 (1997); Wang et al., Journal of Structural Biology. 124, 151-163 (1998); Szyk et al., Journal of Structural Biology. 156, 165-174 (2006)). The internal chamber of this tetradecamer is decorated with fourteen serine protease active sites and is large enough to accommodate a 50 kDa protein. Twelve angstrom-wide pores at both poles of the complex are too narrow to allow entry of most folded proteins into the proteolytic chamber. Thus, accessory ATPases like ClpA, ClpX, ClpL, and ClpC are required to unfold protein substrates of the ClpP protease (see, e.g., Maurizi et al., Methods in Enzymology. 244, 314-331 (1994); Thompson et al., Journal of Biological Chemistry. 269, 18209-18215 (1994); Maurizi et al., Biochemistry. 37, 7778-7786 (1998); Kessel et al., Journal of Molecular Biology. 250, 587-594 (1995)). Under normal conditions, this fourteen-subunit protease selectively degrades damaged and misfolded proteins through a physical and functional association with accessory ATPases that recognize and unfold its substrates (FIG. 6) (see, e.g., Gottesman, Annual Review of Cell and Developmental Biology. 19, 565-587 (2003); Baker et al., Trends Biochemical Sciences. 31, 647-653 (2006); Singh et al., Proceedings of the National Academy of Science, USA. 97, 8898-8903 (2000); Hsiung et al., FEBS Letters. 581, 3749-3757 (2007)). The binding of the enopeptins to ClpP blocks its association with accessory ATPases (see, e.g., World Health Organization (WHO) Geneva, World Health Report 2002; Nathan, Nature, 431, 899 (2004)). Instead of inhibiting the ATPase-dependent activity of ClpP, the enopeptins apparently reprogram ClpP, switching it from a regulated to an uncontrolled protease. The bactericidal activity of the enopeptins results from the fact that enopeptin-bound ClpP indiscriminately degrades nascent peptides as they emerge from the ribosome (see, e.g., Brötz-Oesterhelt et al., Nature Medicine, 10, 1082-1087 (2005); Kirstein et al., EMBO Molecular Medicine. 1, 37-49; Lee et al., Nature Structural Biology (2010) 17:471-479). Unlike most antibiotics which inhibit macromolecular function, the enopeptins activate their cellular target.

The exceptionally low MICs of the enopeptins against bacteria implies that they have a very high affinity for ClpP. Recent structural studies revealed the manner in which an enopeptin and a synthetic derivative thereof bind to ClpP (see, e.g., Lee supra). In the crystal structures of enopeptin-Clp complexes, the antibiotics bind at the interfaces between ClpP monomers in the tetradecameric complex. They make extensive contacts with the N-terminal hairpin region of ClpP that interacts with accessory ATPases. The proline-rich peptidolactone core structures make multiple hydrophobic contacts with ClpP involving Ile28, Ile90, Tyr112, and Leu189. Additionally, the N-acyl-phenylalanine side chains of the peptidolactones bind in the innermost region between adjacent ClpP monomers. While the N-acyl-phenylalanine side chain of the enopeptins is deeply buried in ClpP, approximately half of their peptidolactone core is solvent accessible. Because it is so deeply buried at the interface between ClpP monomers, we suspect that the N-acyl-phenylalanine side chain of the enopeptins strongly contributes to their high affinity for ClpP. In any case, a comparison of the structures of free ClpP and the enopeptin-bound ClpP makes it clear that the antibiotics induce a “closed-to-open gate” transition of the ClpP N-terminal domains, which exposes the proteolytic chamber of the tetradecamer.

Although the enopeptin natural products have remarkable antibacterial activity in vitro, their chemical lability and poor solubility limit their efficacy in vivo (see, e.g., Brötz-Oesterhelt et al., Nature Medicine, 10, 1082-1087 (2005); Hinzen et al., Chem Med Chem. 1, 689-693 (2006)). In an effort to improve the pharmacological properties of the enopeptins, a research group at Bayer Healthcare AG carried out an intensive effort to optimize the structures of the enopeptins. Their medicinal chemistry program was guided in part by the observation that the conformation of the peptidolactone core structure was constrained by two transannular hydrogen bonds to the phenylalanine moiety of the side chain. On this basis, it was anticipated that replacing the constituents of the peptidolactone with conformationally restricted amino acids would yield enopeptin derivatives with improved antibacterial activity. Most amino acid substitutions in the peptidolactone core structure decreased antibacterial activity, but replacement of the N-methylalanine moiety with a more conformationally restricted pipecolate moiety yielded a more potent analogue. Presumably, rigidification of the peptidolactone lowers the entropic cost of binding to the ClpP core. The stability and antibacterial activity of these rigidified enopeptin analogs were further enhanced by replacement of the exocyclic phenylalanine with 3,5-difluorophenylalanine and by substitution of the polyunsaturated side chain with long chain α,β-unsaturated amides. One optimized enopeptin derivative, known as acyldepsipeptide 4 (ADEP 4) (FIG. 1), exhibited remarkable activity both in vitro and in vivo. As was the case for the parent enopeptins, no cross-resistance to ADEP 4 and the other synthetic derivatives of the enopeptins was observed; the compounds were active against multi-drug resistant pathogens (see, e.g., Brötz-Oesterhelt et al., Nature Medicine, 10, 1082-1087 (2005); Hinzen et al., Chem Med Chem. 1, 689-693 (2006); Kirstein et al., EMBO Molecular Medicine. 1, 37-49; Lee et al., Nature Structural Biology (2010) 17:471-479). ADEP4 and other synthetic derivatives of the enopeptins were shown to clear methicillin-resistant Staphylococcus aureus, vancomycin-resistant E. faecalis, and Streptococcus pneumoniae infections in both mice and rats. Mice infected with a lethal innocula of Enterococcus faecalis had a 100% survival rate when treated with a single dose of ADEP 4 at 0.5 mg/kg. Remarkably, the minimum inhibitory concentration (MIC) and in vivo antibacterial activity of ADEP 4 equaled or even surpassed that of linezolid, an FDA approved antibacterial drug.

Despite their promising activity and efficacy in mouse models of infection, Bayer Healthcare AG has not pursued clinical development of the acyldepsipeptides. The group at Bayer predicted that the acyldepsipeptides would have limited clinical utility because enopeptin-resistant bacteria are observed at a relatively high frequency (10⁻⁶) (see, e.g., Brötz-Oesterhelt, supra). The high frequency of spontaneous enopeptin resistance may be reflective of the fact that clpP is dispensable for viability (see, e.g., Kwon et al., Infection and Immunity. 71, 2757-3765 (2003); Kwon et al., Infection and Immunity. 72, 56460-5653 (2004); Robertson et al., Journal of Bacteriology. 184, 3508-3520 (2002); Gaillot et al., Molecular Microbiology. 35, 1286-1294 (2000); Webb et al., Molecular Microbiology. 34,112-123 (1999); Frees et al., Molecular Microbiology. 48, 1565-78 (2003); Frees et al., Infection Immunity. 73, 8100-8 (2005)). Using E. coli as a model system, Bayer found that enopeptin-resistant strains often have loss-of-function mutations in the clpP gene. One enopeptin-resistant mutant of E. coli that they characterized had a missense mutation in the clpP gene that resulted in a threonine to alanine substitution at position 182 (see, e.g., Brötz-Oesterhelt, supra). The proximity of this substitution to the ClpP active site was invoked to explain the catalytic inactivity of the protease. Because ClpP is not essential for viability and the antibacterial activity of the enopeptins requires a functional ClpP, it is anticipated that loss-of-function mutations in the clpP gene will be common in enopeptin-resistant bacteria. As is the case for other antibacterial drugs with high rates of resistance (e.g., rifampicin), it has been proposed that the enopeptins may be most effective as part of combination therapy with other antibacterial drugs (see, e.g., Kirstein, supra). However, systematic studies of the enopeptin derivatives in complex with other antibacterial drugs has not yet been reported.

The enopeptin antibiotics and their synthetic derivatives are a remarkable group of drug leads that satisfy many of the criteria of conventional drug discovery programs. They have potent activity against troublesome, multi-drug resistant pathogens (i.e., MICs are less than 1 mg/mL) (see, e.g., Brötz-Oesterhelt et al., Nature Medicine, 10, 1082-1087 (2005); Hinzen et al., Chem Med Chem. 1, 689-693 (2006)). They target a protein that is not bound by any other clinically used antibacterial drugs (i.e., the ClpP protease is a novel target) and have an unprecedented mechanism of action (i.e., activation of proteolysis). They are not toxic to eukaryotes and can be safely used to treat infections in mice. In the context of conventional drug discovery programs, the critical flaw of the enopeptin antibiotics is that resistant-bacteria are observed at a high frequency. We propose that these acyldepsipeptides have two features that make them great candidates for anti-virulence programs. First, the antibiotics bind to the accessory ATPase binding site on ClpP that is must be accessible for ClpP to have its normal physiological function. Any compound that blocks the association of ClpP with its accessory ATPases will be an inhibitor of ClpP function and as such will be an inhibitor of virulence factor production. Mechanism-based inhibitors of ClpP are known to block virulence factor production in MRSA and infectivity in L. monocytogenes (see, e.g., Böttcher et al., Journal of the American Chemical Society. 130, 14400-14401 (2008); Böttcher et al., Chem Bio Chem, 10, 663-666 (2009); Böttcher et al., Chem Med Chem. 4, 1260-1263 (2009); Osada et al., Journal of Antibiotics. 44, 1463-1466 (1991)). Thus, we hypothesize that the structure of the enopeptin-ClpP complex can be used as the basis for the design of novel ClpP ligands that do not activate the enzyme's proteolytic activity. One would anticipate that such compounds would lack antibacterial activity, but would block virulence factor production by pathogens. Second, while drug resistance is generally has disastrous consequences in clinical settings, we hypothesize that resistance to the acyldepsipeptides will be advantageous with respect to clearing infections. Since resistance to the acyldepsipeptides has been ascribed to loss of function mutations in the clpP gene and a functional clpP gene is required by many pathogenic bacteria for virulence factor production (including Salmonella typhimurium, Listeria monocytogenes, Streptococcus pneumonia, and Staphylococcus aureus strains) (see, e.g., Kwon et al., Infection and Immunity. 71, 2757-3765 (2003); Kwon et al., Infection and Immunity. 72, 56460-5653 (2004); Robertson et al., Journal of Bacteriology. 184, 3508-3520 (2002); Gaillot et al., Molecular Microbiology. 35, 1286-1294 (2000); Webb et al., Molecular Microbiology. 34,112-123 (1999); Frees et al., Molecular Microbiology. 48, 1565-78 (2003); Frees et al., Infection Immunity. 73, 8100-8 (2005)), we hypothesize that acyldepsipeptide-resistant bacteria will be avirulent. Thus, the use of acyldepsipeptides as antibacterial drugs could initially cure bacterial infections and ultimately drive the evolution of drug-resistant bacteria that do not cause disease.

(i) Synthesize and Evaluate the Capacity of Acyldepsipeptide Derivatives to Affect Antibacterial Activity and/or Virulence Factor Production in Pathogenic Bacteria.

Based on the structure of the enopeptins, we successfully designed an analog with enhanced antibacterial activity. The recently published crystal structure of the acyldepsipeptide in complex with B. subtilis ClpP provides additional opportunities for structure-based design (FIGS. 7A-7B) (see, e.g., Lee et al., Nature Structural Biology (2010) 17:471-479). It is likely that structure-based design and synthesis will be able to yield either enhanced activators of ClpP activity or inhibitors of ClpP activity. Enopeptin analogs that form additional contacts with ClpP will bind more tightly and thus activate its activity more strongly. In contrast, enopeptin analogs that have lower affinity for the ATPase binding site of ClpP than the parent compounds are likely to be inhibitors of the protease's activity. These compounds will not have antibacterial activity, but they will block the ClpP-dependent virulence. Inhibition of ClpP is known to block virulence in S. aureus and L. monocytogenes (see, e.g., Böttcher et al., Journal of the American Chemical Society. 130, 14400-14401 (2008); Böttcher et al., Chem Bio Chem, 10, 663-666 (2009); Böttcher et al., Chem Med Chem. 4, 1260-1263 (2009); Osada et al., Journal of Antibiotics. 44, 1463-1466 (1991)).

(ii) Rational Modification of the N-acyl-phenylalalnine Moiety will Yield Enopeptin Analogs having Enhanced Antibacterial Activity or Anti-Virulence Activity.

We will examine a variety of enopeptin derivatives, including those that we recently reported do not have antibacterial activity. The structurally similarities of these compounds to those that have antibacterial activity suggests that they may retain their ability to bind ClpP. Additional ClpP ligands will be rationally designed and synthesized. The recently published structure of B. subtilis ClpP in complex with an optimized enopeptin derivative called ADEP 2 will be used in the rational design (FIG. 7B) (see, e.g., Lee et al., Nature Structural Biology (2010) 17:471-479). We hypothesize that the ideal target for modification is the acyl 3,5-difuorophenylalanine moiety of ADEP 2. As it is deeply buried at the interface between ClpP monomers, the acyl 3,5-difluorophenylalanine side chain of ADEP2 is a significant contributor to high affinity binding of the molecule to ClpP. The α,β-unsaturation of the acyl group is critical for activity and the two fluorine atoms dramatically enhance activity of ADEP 2. Targeted modifications of (1) the unsaturated unit or (2) the 3,5-difluorophenyl moiety should yield small molecules with either higher and lower affinity for ClpP. For example, a compound containing a saturated acyl group may bind ClpP with insufficient for ClpP activation,but sufficient affinity to compete for the ATPase binding site. This same analysis can be applied to the difluorophenylalanine appended to ADEP 2. One fluorine atom is well accommodated in a polar environment formed by the main chain acyl of Asp78 and the β-hydroxy group of Thr79. Replacement of this group with hydrogen bond donors, like an amino group or a hydroxyl group, could yield higher affinity ClpP ligands since they will likely form hydrogen bonds to Asp78 and Thr79 (FIG. 8). In contrast, derivatives lacking the side chain entirely or with bulky non-polar substituents on the phenyalanine moiety are likely to have lower affinity for ClpP (FIG. 8). We hypothesize that the enopeptin derivatives with low affinity for ClpP will not have bactericidal activity, but inhibit virulence factor production via competitive binding to the ATPase site of ClpP. Accordingly, hypothesize that the enopeptin derivatives with high affinity for ClpP will have enhanced bactericidal activity.

Minimum inhibitory concentration (MIC) determinations will be conducted using proven methodologies described in documents published by The Clinical and Laboratory Standards Institute (CLSI). MICs will be determined in duplicate using serial dilution (see, e.g., Performance standards for antimicrobial susceptibility testing; Sixteenth informational supplement. M100-S16. Clinical Laboratory Standards Institute (formerly NCCLS), Wayne, Pa. (2006)). Prototype ATCC strains of Enterococcus faecium (ATCC 29212), methicillin-susceptible Staphylococcus aureus (ATCC 35556), and methicillin-resistant Staphylococcus aureus (ATCC 43300). We will measure the properties of novel antibiotics against panels of clinical isolates (i.e., those obtained from hospitalized patients). The clinical isolates provide a better assessment of the true potential of an investigational agent. The panel of clinical isolates, numbering in the hundreds and representing diverse types of Gram-positive bacteria, was obtained by random samplings from patient blood, sputum, tissue, and urine at the Veterans Affairs Medical Center in Providence, R.I. (June 2004 through July 2010).

To follow up on our finding that the minimal bactericidial concentrations of the enopeptin derivatives are nearly identical to the minimal inhibitory concentrations, we plan to carry out time kill kinetic assays. These time-kill experiments will be used to more fully measure and classify antibiotic activities. These studies will use the prototype ATCC isolates described above. Each time-kill will be preformed in duplicate and bacterial quantification of all samples were preformed as previously described (see, e.g., Socha et al., Bioorg Med Chem. 14: 8446-54 (2006)). All antimicrobial agents will be tested at two times their respective MIC with a starting inoculum of 5×10⁵ CFU/mL. Colony counts will be determined by plating 20 μL of each diluted sample onto TSA plates in triplicate, followed by incubation at 35° C. for 24 h. This methodology has a lower limit of detection of 2.0 log₁₀ CFU/ml. Growth control wells for each organism will be prepared without antibiotic and run in parallel to the antibiotic test wells. Bactericidal activity (99.9% kill) is defined as a ≧3 log₁₀ CFU/ml reduction in bacterial density from the starting inoculum (see, e.g., LaPlante et al., Antimicrob Agents Chemother 48:4665-72 (2004)). Time to 99.9% kill will be determined by linear regression of the sample points if r²≧0.95 or by visual inspection.

We hypothesize that any enopeptin derivative that does not have antibacterial activity may still retain the ability to bind to ClpP in vitro and in vivo. The acyldepsipeptide analogs lacking antibacterial activity will be tested for their ability to block the binding of ClpP to accessory ATPases in vitro. For these analyses, we will use size exclusion chromatography using purified ClpP, MecA, and ClpC, as described by Kirstein et al., EMBO Molecular Medicine. 1, 37-49. These three proteins are known to form a high molecular weight complex that dissociates in the presence of the acyldepsipeptides. In the presence of the enopeptin-binding acyldepsipeptides, two discrete species corresponding to the ClpP tetradecamer and the MecA-ClpC complex are observed. Compounds of interest are those that trigger disassembly of the complex via competition for the ATPase binding site of ClpP. This analytical method will unambiguously determine if any synthetic compounds trigger disruption of this complex. The successes of size exclusion chromatography in biophysical analyses of ClpP suggest that these approaches will be an ideal means by which to identify ClpP ligands. The shape of the curve and other data from these analyses will also reveal differences in the degrees to which enopeptin derivatives trigger ClpP complex disassembly (kinetic analyses). These experiments, which are well described and straightforward, will be carried out with a fast protein liquid chromatograph (FPLC). Although this is not a high-throughput assay, the small number of compounds (<15) makes this approach tenable.

Any compounds of interest identified as ClpP ligands in the primary screen will be tested to determine if they affect viability and virulence factor production in the aforementioned in vivo and in vitro assays (see, e.g., Böttcher et al., Journal of the American Chemical Society, 130, 14400-14401 (2008); Böttcher et al., Chem Bio Chem, 10, 663-666 (2009); Brötz-Oesterhelt et al., Nature Medicine, 10, 1082-1087 (2005)). For the in vitro experiments, virulence factor expression by S. aureus will be assessed using plate-based assays based on pathogen-mediated hemolysis and proteolysis, as well as in lipase and DNase activity assays. In parallel, it will be determined if the compounds interfere with the virulence of pathogens in mouse models of Staphylococcus aureus infections. As described by the research group at Bayer Healthcare AG, we plan to intraperitoneally inoculate CFW-1 mice with bacterial loads above and below the lethal infective doses (see, e.g., Brötz-Oesterhelt, supra). The mice will be treated with small molecules of interest once intraperitoneally 30 minutes after the infection. Five animals will be used per treatment group and monitored for five days to assess survival. For determination of colony-forming units in the mice, their organs will be removed 6 h after infection and homogenized. The bacteria in the homogenates will be counted on agar plates. Statistical analyses using the Mann-Whitney test will be used for CFU determination and the log-rank test will be used to generate survival models.

Other Embodiments

All patents, patent applications, and literature references cited herein are incorporated herein by reference.

The foregoing has been a description of certain nonlimiting embodiments of the invention. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims. 

What is claimed is:
 1. A compound of Formula (VI):

or a pharmaceutically acceptable salt thereof; wherein: R¹ is hydrogen or —CH₃; R³ and R⁴ are joined to form a substituted 6-membered heterocyclyl; R⁵ is

x is an integer between 1 and 10, inclusive; R^(10a) and R^(10b) are independently hydrogen or optionally substituted alkyl; R⁹ is hydrogen, halogen, —CN, —NO₂, —N₃, substituted hydroxyl, substituted thiol, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; each instance of R⁶ is independently halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; m is 0 or an integer of between 1 and 5, inclusive; R¹¹ is hydrogen; and R¹² is hydrogen, optionally substituted alkyl, or optionally substituted carbocyclyl.
 2. A compound of claim 1, wherein the compound is of Formula (III-b):

or a pharmaceutically acceptable salt thereof; wherein: each instance of R⁷ is independently halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; and n is an integer of between 1 and 8, inclusive.
 3. The compound of claim 1, wherein the compound is selected from the group consisting of:

and pharmaceutically acceptable salts thereof.
 4. The compound of claim 1, wherein x is
 1. 5. The compound of claim 4, wherein each of R^(10a) and R^(10b) is hydrogen; and R⁹ is optionally substituted alkyl.
 6. The compound of claim 1, wherein R¹² is optionally substituted alkyl.
 7. The compound of claim 6, wherein R¹² is —CH₃.
 8. The compound of claim 1, wherein m is 2 and the group:


9. The compound of claim 1, wherein m is 1 and the group:


10. The compound of claim 2, wherein n is
 1. 11. A method of preparing a compound of Formula (I), the method comprising providing a compound of Formula (G):

or salt thereof; and coupling the compound of Formula (G), or salt thereof, with a compound of Formula (H):

or salt thereof; to provide a compound of Formula (I):

or salt thereof; wherein: R² is hydrogen and the stereochemistry of the carbon attached to R² and R³ is:

R¹ is hydrogen or CH₃; R³ and R⁴ are joined to form a substituted 6-membered heterocyclyl; R⁵ is

x is an integer between 1 and 10, inclusive; R^(10a) and R^(10b) are independently hydrogen or optionally substituted alkyl; R⁹ is hydrogen, halogen, —CN, —NO₂, —N₃, substituted hydroxyl, substituted thiol, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; each instance of R⁶ is independently halogen, —OH, —SH, —NH₂, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, substituted hydroxyl, substituted thiol, substituted amino, sulfonyl, sulfinyl, acyl, silyl, boronyl, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted carbocyclyl, optionally substituted heterocyclyl, optionally substituted aryl, or optionally substituted heteroaryl; m is 0 or an integer of between 1 and 5, inclusive; R¹¹ is hydrogen; and R¹² is hydrogen, optionally substituted alkyl, or optionally substituted carbocyclyl.
 12. A pharmaceutical composition comprising an effective amount of a compound of claim 1, or pharmaceutically acceptable salt thereof, and, optionally, a pharmaceutically acceptable excipient.
 13. A method of treating a microbial infection in a subject comprising administering an effective amount of a compound of claim 1, or pharmaceutically acceptable salt thereof, to the subject.
 14. The method of claim 13, wherein the microbial infection is a bacterial infection.
 15. The method of claim 14, further comprising administering the compound, or pharmaceutically acceptable salt thereof, in combination with an antibiotic.
 16. The method of claim 15, wherein the antibiotic is a ribosome-targeting antibiotic.
 17. The method of claim 14, wherein the bacterial infection is resistant to other treatments.
 18. The method of claim 14, wherein the bacterial infection is multi-drug tolerant or multi-drug resistant.
 19. A method of treating microbial virulence comprising contacting an effective amount of a compound of claim 1, or pharmaceutically acceptable salt thereof, to a microorganism.
 20. The method of claim 19, wherein the compound, or pharmaceutically acceptable salt thereof, blocks virulence factor production. 